Commit ac42f34d authored by Jerome Mariette's avatar Jerome Mariette
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parent 9ea9385a
......@@ -22,13 +22,13 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="params" value=" "|explode:$analyse.params}
<ul>
{assign var="score_index" value=$params|@array_keys:"--score"}
<li>{$llang.AdaptorcleanerAnalyse_minscore|replace:"###MIN_SCORE###":$params[$score_index[0]+1]}</li>
<li class="parameter">{$llang.AdaptorcleanerAnalyse_minscore|replace:"###MIN_SCORE###":$params[$score_index[0]+1]}</li>
{assign var="match_index" value=$params|@array_keys:"--match"}
<li>{$llang.AdaptorcleanerAnalyse_minmatch|replace:"###MIN_MATCH###":$params[$match_index[0]+1]}</li>
<li> class="parameter"{$llang.AdaptorcleanerAnalyse_minmatch|replace:"###MIN_MATCH###":$params[$match_index[0]+1]}</li>
{assign var="len_index" value=$params|@array_keys:"--minlen"}
<li>{$llang.AdaptorcleanerAnalyse_minlen|replace:"###MIN_LEN###":$params[$len_index[0]+1]}</li>
<li class="parameter">{$llang.AdaptorcleanerAnalyse_minlen|replace:"###MIN_LEN###":$params[$len_index[0]+1]}</li>
{if $analyse_results["all"]["default"]["adaptor_file"] == ""}
<li>{$llang.AdaptorcleanerAnalyse_adaptor} <br />
<li class="parameter">{$llang.AdaptorcleanerAnalyse_adaptor} <br />
{$isseq=false}
{foreach $params as $param}
{if $isseq}
......@@ -43,7 +43,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
{else}
{assign var="index" value=$params|@array_keys:"--adaptor"}
<li>{$llang.AdaptorcleanerAnalyse_adaptor}
<li class="parameter">{$llang.AdaptorcleanerAnalyse_adaptor}
<br />
<div class="file-display">{$analyse_results["all"]["default"]["adaptor_file"]}</div>
</li>
......
......@@ -45,7 +45,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div class="underline"> </div>
{block name=params_content}
<ul>
<li>{$analyse.params}</li>
<li class="parameter">{$analyse.params}</li>
</ul>
{/block}
{/if}
......
......@@ -21,8 +21,8 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
<ul>
<li>{$params[0]}</li>
<li>{$params[1]}</li>
<li class="parameter">{$params[0]}</li>
<li class="parameter">{$params[1]}</li>
</ul>
{/block}
......
......@@ -25,9 +25,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="max_index" value=$params|@array_keys:"-M"}
{assign var="adaptor_index" value=$params|@array_keys:"-a"}
<ul>
<li>{$llang.CutAdaptAnalyse_error_rate|replace:"###ERROR_RATE###":$params[$error_index[0]+1]}</li>
<li>{($llang.CutAdaptAnalyse_len|replace:"###MIN_LEN###":$params[$min_index[0]+1])|replace:"###MAX_LEN###":$params[$max_index[0]+1]}</li>
<li>{$llang.CutAdaptAnalyse_adaptors|replace:"###ADAPTOR_USED###":$params[$adaptor_index[0]+1]}</li>
<li class="parameter">{$llang.CutAdaptAnalyse_error_rate|replace:"###ERROR_RATE###":$params[$error_index[0]+1]}</li>
<li class="parameter">{($llang.CutAdaptAnalyse_len|replace:"###MIN_LEN###":$params[$min_index[0]+1])|replace:"###MAX_LEN###":$params[$max_index[0]+1]}</li>
<li class="parameter">{$llang.CutAdaptAnalyse_adaptors|replace:"###ADAPTOR_USED###":$params[$adaptor_index[0]+1]}</li>
</ul>
{/block}
......
......@@ -23,9 +23,9 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="filter_index" value=$params|@array_keys:"--keep"}
<ul>
{if $params[$filter_index[0]+1] == "N"}
<li>{$llang.FastqIlluminaFilterAnalyse_Nparams}</li>
<li class="parameter">{$llang.FastqIlluminaFilterAnalyse_Nparams}</li>
{else}
<li>{$llang.FastqIlluminaFilterAnalyse_Yparams}</li>
<li class="parameter">{$llang.FastqIlluminaFilterAnalyse_Yparams}</li>
{/if}
</ul>
{/block}
......
......@@ -26,19 +26,19 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{if in_array("-m", $params)}
{assign var="mindex" value=$params|@array_keys:"-m"}
<li>{$llang.FlashAnalyse_min_overlap|replace:"###MINOVERLAP###":$params[$mindex[0]+1]}</li>
<li class="parameter">{$llang.FlashAnalyse_min_overlap|replace:"###MINOVERLAP###":$params[$mindex[0]+1]}</li>
{/if}
{if in_array("-M", $params)}
{assign var="m2index" value=$params|@array_keys:"-M"}
<li>{$llang.FlashAnalyse_max_overlap|replace:"###MAXOVERLAP###":$params[$m2index[0]+1]}</li>
<li class="parameter">{$llang.FlashAnalyse_max_overlap|replace:"###MAXOVERLAP###":$params[$m2index[0]+1]}</li>
{/if}
{if in_array("-x", $params)}
{assign var="xindex" value=$params|@array_keys:"-x"}
<li>{$llang.FlashAnalyse_mismatch_ratio|replace:"###MISMATCHRATIO###":$params[$xindex[0]+1]}</li>
<li class="parameter">{$llang.FlashAnalyse_mismatch_ratio|replace:"###MISMATCHRATIO###":$params[$xindex[0]+1]}</li>
{/if}
{if in_array("-p", $params)}
{assign var="pindex" value=$params|@array_keys:"-p"}
<li>{$llang.FlashAnalyse_phred_offset|replace:"###PHREDOFFSET###":$params[$pindex[0]+1]}</li>
<li class="parameter">{$llang.FlashAnalyse_phred_offset|replace:"###PHREDOFFSET###":$params[$pindex[0]+1]}</li>
{/if}
</ul>
{/block}
......
......@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="params" value=";"|explode:$analyse.params}
<ul>
{foreach from=$params item=param}
<li>{$param}</li>
<li class="parameter"am}</li>
{/foreach}
</ul>
{/block}
......
......@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="params" value=";"|explode:$analyse.params}
<ul>
{foreach from=$params item=param}
<li>{$param}</li>
<li class="parameter">{$param}</li>
{/foreach}
</ul>
{/block}
......
......@@ -22,7 +22,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="params" value=";"|explode:$analyse.params}
<ul>
{foreach from=$params item=param}
<li>{$param}</li>
<li class="parameter">{$param}</li>
{/foreach}
</ul>
{/block}
......
......@@ -23,16 +23,16 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{if in_array("--clean-length-std", $params)}
{assign var="index" value=$params|@array_keys:"--std"}
<li>{$llang.PyrocleanerAnalyse_length_std_param|replace:"###STD###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_length_std_param|replace:"###STD###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-length-win", $params)}
{assign var="min_index" value=$params|@array_keys:"--min"}
{assign var="max_index" value=$params|@array_keys:"--max"}
<li>{($llang.PyrocleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
<li class="parameter">{($llang.PyrocleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
{/if}
{if in_array("--clean-ns", $params)}
{assign var="index" value=$params|@array_keys:"--ns_percent"}
<li>{$llang.PyrocleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-complexity-win", $params)}
{assign var="win_index" value=$params|@array_keys:"--window"}
......@@ -42,23 +42,23 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/if}
{if in_array("--clean-complexity-full", $params)}
{assign var="index" value=$params|@array_keys:"--complexity"}
<li>{$llang.PyrocleanerAnalyse_complexity_full_param|replace:"###COMPLEXIT_RATIO###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_complexity_full_param|replace:"###COMPLEXIT_RATIO###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-quality", $params)}
{assign var="index" value=$params|@array_keys:"--quality-threshold"}
<li>{$llang.PyrocleanerAnalyse_qual_param|replace:"###MIN_QUAL###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_qual_param|replace:"###MIN_QUAL###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-duplicated-reads", $params) AND in_array("--aggressive", $params)}
{assign var="index" value=$params|@array_keys:"--duplication_limit"}
<li>{$llang.PyrocleanerAnalyse_duplication_aggressive_param|replace:"###SIZE_LIMIT###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_duplication_aggressive_param|replace:"###SIZE_LIMIT###":$params[$index[0]+1]}</li>
{elseif in_array("--clean-duplicated-reads", $params)}
{assign var="index" value=$params|@array_keys:"--duplication_limit"}
<li>{$llang.PyrocleanerAnalyse_duplication_param|replace:"###SIZE_LIMIT###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.PyrocleanerAnalyse_duplication_param|replace:"###SIZE_LIMIT###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-pairends", $params)}
{assign var="border_index" value=$params|@array_keys:"--border-limit"}
{assign var="match_index" value=$params|@array_keys:"--missmatch"}
<li>{($llang.PyrocleanerAnalyse_pairend_param|replace:"###BORDER_LIMIT###":$params[$border_index[0]+1])|replace:"###MIN_MATCHES###":$params[$match_index[0]+1]}</li>
<li class="parameter">{($llang.PyrocleanerAnalyse_pairend_param|replace:"###BORDER_LIMIT###":$params[$border_index[0]+1])|replace:"###MIN_MATCHES###":$params[$match_index[0]+1]}</li>
{/if}
</ul>
{/block}
......
......@@ -21,7 +21,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=params_content}
{assign var="params" value=" "|explode:$analyse.params}
<ul>
<li>{$analyse.params}</li>
<li class="parameter">{$analyse.params}</li>
</ul>
{/block}
......
......@@ -26,11 +26,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{* Filter on min number of matches *}
{if in_array("--fwd-minmatch", $params)}
{assign var="min_fwd_index" value=$params|@array_keys:"--fwd-minmatch"}
<li>{($llang.S16CleanerAnalyse_fwd_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MIN_FWD###":$params[$min_fwd_index[0]+1]}</li>
<li class="parameter">{($llang.S16CleanerAnalyse_fwd_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MIN_FWD###":$params[$min_fwd_index[0]+1]}</li>
{* Filter on max number of errors *}
{else}
{assign var="max_fwd_index" value=$params|@array_keys:"--fwd-maxerror"}
<li>{($llang.S16CleanerAnalyse_fwd_err_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MAX_FWD###":$params[$max_fwd_index[0]+1]}</li>
<li class="parameter">{($llang.S16CleanerAnalyse_fwd_err_param|replace:"###FWD###":$params[$fwd_index[0]+1])|replace:"###MAX_FWD###":$params[$max_fwd_index[0]+1]}</li>
{/if}
{/if}
{if in_array("--reverse", $params)}
......@@ -38,29 +38,29 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{* Filter on min number of matches *}
{if in_array("--rvrs-minmatch", $params)}
{assign var="min_rvrs_index" value=$params|@array_keys:"--rvrs-minmatch"}
<li>{($llang.S16CleanerAnalyse_rvrs_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MIN_RVRS###":$params[$min_rvrs_index[0]+1]}</li>
<li class="parameter">{($llang.S16CleanerAnalyse_rvrs_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MIN_RVRS###":$params[$min_rvrs_index[0]+1]}</li>
{* Filter on max number of errors *}
{else}
{assign var="max_rvrs_index" value=$params|@array_keys:"--rvrs-maxerror"}
<li>{($llang.S16CleanerAnalyse_rvrs_err_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MAX_RVRS###":$params[$max_rvrs_index[0]+1]}</li>
<li class="parameter">{($llang.S16CleanerAnalyse_rvrs_err_param|replace:"###RVRS###":$params[$rvrs_index[0]+1])|replace:"###MAX_RVRS###":$params[$max_rvrs_index[0]+1]}</li>
{/if}
{/if}
{if in_array("--clean-length", $params)}
{assign var="min_index" value=$params|@array_keys:"--min-length"}
{assign var="max_index" value=$params|@array_keys:"--max-length"}
<li>{($llang.S16CleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
<li class="parameter">{($llang.S16CleanerAnalyse_length_win_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
{/if}
{if in_array("--clean-ns", $params)}
{assign var="index" value=$params|@array_keys:"--ns-percent"}
<li>{$llang.S16CleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.S16CleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-homopolymers", $params)}
{assign var="index" value=$params|@array_keys:"--homopolymers-length"}
<li>{$llang.S16CleanerAnalyse_homopolymer_param|replace:"###HOMO_SIZE###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.S16CleanerAnalyse_homopolymer_param|replace:"###HOMO_SIZE###":$params[$index[0]+1]}</li>
{/if}
{if in_array("--clean-full-length", $params)}
{assign var="index" value=$params|@array_keys:"--full-length-min-size"}
<li>{$llang.S16CleanerAnalyse_full_size_param|replace:"###FULL_MIN_SIZE###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.S16CleanerAnalyse_full_size_param|replace:"###FULL_MIN_SIZE###":$params[$index[0]+1]}</li>
{/if}
</ul>
{/block}
......
......@@ -25,12 +25,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="sample" value=$sample}
{/foreach}
<ul>
<li>{$analyse.params}</li>
<li>{($llang.SFFFileAnalyse_file_content|replace:"###FILE_NAME###":"<strong>###FILE_NAME###</strong>")|replace:"###FILE_NAME###":$params[$index[0]+1]}
<li class="parameter">{$analyse.params}</li>
<li class="parameter">{($llang.SFFFileAnalyse_file_content|replace:"###FILE_NAME###":"<strong>###FILE_NAME###</strong>")|replace:"###FILE_NAME###":$params[$index[0]+1]}
<br />
<div class="file-display">{$analyse_results[$sample]["default"]["config_file"]}</div>
<i> with: mid = "{$llang.Analyse_sample}", "fwd_seq", nb_missmatch, "rvrs_seq";</i>
</li>
</li class="parameter">
</ul>
{/block}
......
......@@ -24,31 +24,31 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{if in_array("--clean-length", $params)}
{assign var="min_index" value=$params|@array_keys:"--min-length"}
{assign var="max_index" value=$params|@array_keys:"--max-length"}
<li>{($llang.SmartkitcleanerAnalyse_length_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
<li class="parameter">{($llang.SmartkitcleanerAnalyse_length_param|replace:"###MIN_SIZE###":$params[$min_index[0]+1])|replace:"###MAX_SIZE###":$params[$max_index[0]+1]}</li>
{/if}
{if in_array("--clean-ns", $params)}
{assign var="ns_index" value=$params|@array_keys:"--ns-percent"}
<li>{$llang.SmartkitcleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$ns_index[0]+1]}</li>
<li class="parameter">{$llang.SmartkitcleanerAnalyse_ns_param|replace:"###NS_PERCENT###":$params[$ns_index[0]+1]}</li>
{/if}
{if in_array("--clean-complexity-win", $params)}
{assign var="win_index" value=$params|@array_keys:"--window"}
{assign var="step_index" value=$params|@array_keys:"--step"}
{assign var="ratio_index" value=$params|@array_keys:"--complexity"}
<li>{(($llang.SmartkitcleanerAnalyse_complexity_win_param|replace:"###WINDOW_SIZE###":$params[$win_index[0]+1])|replace:"###STEP_SIZE###":$params[$step_index[0]+1])|replace:"###COMPLEXIT_RATIO###":$params[$ratio_index[0]+1]}</li>
<li class="parameter">{(($llang.SmartkitcleanerAnalyse_complexity_win_param|replace:"###WINDOW_SIZE###":$params[$win_index[0]+1])|replace:"###STEP_SIZE###":$params[$step_index[0]+1])|replace:"###COMPLEXIT_RATIO###":$params[$ratio_index[0]+1]}</li>
{/if}
{if in_array("--clean-complexity-full", $params)}
{assign var="index" value=$params|@array_keys:"--complexity"}
<li>{$llang.SmartkitcleanerAnalyse_complexity_full_param|replace:"###COMPLEXIT_RATIO###":$params[$index[0]+1]}</li>
<li class="parameter">{$llang.SmartkitcleanerAnalyse_complexity_full_param|replace:"###COMPLEXIT_RATIO###":$params[$index[0]+1]}</li>
{/if}
{assign var="seq1_index" value=$params|@array_keys:"--primer1"}
{assign var="match1_index" value=$params|@array_keys:"--primer1-minmatch"}
{assign var="score1_index" value=$params|@array_keys:"--primer1-score"}
{assign var="undef1_index" value=$params|@array_keys:"--primer1-undef"}
<li>{((($llang.SmartkitcleanerAnalyse_adapt1|replace:"###ADAPT1_SEQ###":$params[$seq1_index[0]+1])|replace:"###ADAPT1_MATCHES###":$params[$match1_index[0]+1])|replace:"###ADAPT1_SCORE###":$params[$score1_index[0]+1])|replace:"###ADAPT1_UNDEF###":$params[$undef1_index[0]+1]}</li>
<li class="parameter">{((($llang.SmartkitcleanerAnalyse_adapt1|replace:"###ADAPT1_SEQ###":$params[$seq1_index[0]+1])|replace:"###ADAPT1_MATCHES###":$params[$match1_index[0]+1])|replace:"###ADAPT1_SCORE###":$params[$score1_index[0]+1])|replace:"###ADAPT1_UNDEF###":$params[$undef1_index[0]+1]}</li>
{assign var="seq2_index" value=$params|@array_keys:"--primer2"}
{assign var="match2_index" value=$params|@array_keys:"--primer2-minmatch"}
{assign var="score2_index" value=$params|@array_keys:"--primer2-score"}
<li>{(($llang.SmartkitcleanerAnalyse_adapt2|replace:"###ADAPT2_SEQ###":$params[$seq2_index[0]+1])|replace:"###ADAPT2_MATCHES###":$params[$match2_index[0]+1])|replace:"###ADAPT2_SCORE###":$params[$score2_index[0]+1]}</li>
<li class="parameter">{(($llang.SmartkitcleanerAnalyse_adapt2|replace:"###ADAPT2_SEQ###":$params[$seq2_index[0]+1])|replace:"###ADAPT2_MATCHES###":$params[$match2_index[0]+1])|replace:"###ADAPT2_SCORE###":$params[$score2_index[0]+1]}</li>
</ul>
{/block}
......
......@@ -25,18 +25,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
<ul>
{if in_array("--trim", $params)}
<li>{$llang.SplitbcAnalyse_trim_param}</li>
<li class="parameter">{$llang.SplitbcAnalyse_trim_param}</li>
{/if}
{if in_array("--mismatches", $params)}
{assign var="mindex" value=$params|@array_keys:"--mismatches"}
<li>{$llang.SplitbcAnalyse_nb_missmatch|replace:"###MISSMATCH###":$params[$mindex[0]+1]}</li>
<li class="parameter">{$llang.SplitbcAnalyse_nb_missmatch|replace:"###MISSMATCH###":$params[$mindex[0]+1]}</li>
{/if}
{if in_array("--partial", $params)}
{assign var="pindex" value=$params|@array_keys:"--partial"}
<li>{$llang.SplitbcAnalyse_nb_partial|replace:"###PARTIAL###":$params[$pindex[0]+1]}</li>
<li class="parameter">{$llang.SplitbcAnalyse_nb_partial|replace:"###PARTIAL###":$params[$pindex[0]+1]}</li>
{/if}
{assign var="index" value=$params|@array_keys:"--bcfile"}
<li>{$llang.SplitbcAnalyse_barecode_used}
<li class="parameter">{$llang.SplitbcAnalyse_barecode_used}
<br />
<div class="file-display">{$analyse_results["barecode_file"]["default"]["barecode_file"]}</div>
</li>
......
......@@ -174,6 +174,7 @@ table.tx-nG6-pi1-listrow tr.tx-nG6-pi1-listrowlast{
}
table.tx-nG6-pi1-listrow td { border-bottom: 1px solid #ddd; }
ul li.filelist { list-style: none; margin-left: 10px; padding-left: 17px; background: url(../img/ico-fleche.png) left 4px no-repeat; }
ul li.parameter { list-style: none; margin-left: 10px; padding-left: 17px; background: url(../img/ico-fleche.png) left 4px no-repeat; }
.tx-nG6-pi1-hidden { color:#9a9a9a; }
.tx-nG6-pi1-hidden a { color:#aacbfb; }
.tx-nG6-pi1-help {
......
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