Commit 625290d1 authored by Jerome Mariette's avatar Jerome Mariette
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parent 8d3232d0
......@@ -19,42 +19,37 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=params_title} Mothur commands and parameters used {/block}
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
{foreach from=$analyse_results key=sample item=sample_results}
{assign var="sample" value=$sample}
{/foreach}
{assign var="args_cmd" value=","|explode:$analyse.params}
<ul>
{foreach from=$params item=param}
{assign var="args_cmd" value=","|explode:$param}
<li class="parameter">{$param}</li>
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
<ul>
{if in_array("qaverage", $params_cmd)}
{assign var="qaverage_index" value=$params_cmd|@array_keys:"qaverage"}
<li class="parameter">Remove sequences that have an average below {$params_cmd[$qaverage_index[0]+1]}.</li>
{/if}
{if in_array("maxambig", $params_cmd)}
{assign var="maxambig_index" value=$params_cmd|@array_keys:"maxambig"}
<li class="parameter">Cull sequences with have {$params_cmd[$maxambig_index[0]+1]} ambiguous bases.</li>
{/if}
{if in_array("maxhomop", $params_cmd)}
{assign var="maxhomop_index" value=$params_cmd|@array_keys:"maxhomop"}
<li class="parameter">Clean reads with homopolymers with a size higher than {$params_cmd[$maxhomop_index[0]+1]}.</li>
{/if}
{if in_array("minlength" , $params_cmd)}
{assign var="minlength_index" value=$params_cmd|@array_keys:"minlength"}
{assign var="maxlength_index" value=$params_cmd|@array_keys:"maxlength"}
<li class="parameter">Clean reads with a length not in between [{$params_cmd[$minlength_index[0]+1]};{$params_cmd[$maxlength_index[0]+1]}].</li>
{/if}
{if in_array("pdiffs", $params_cmd)}
{assign var="pdiffs_index" value=$params_cmd|@array_keys:"pdiffs"}
<li class="parameter">The maximum number of differences allowed with the primer is {$params_cmd[$pdiffs_index[0]+1]|replace:')':''}.</li>
{/if}
</ul>
{/foreach}
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
{if in_array("qaverage", $params_cmd)}
{assign var="qaverage_index" value=$params_cmd|@array_keys:"qaverage"}
<li class="parameter">Remove sequences with a quality average below {$params_cmd[$qaverage_index[0]+1]}.</li>
{/if}
{if in_array("maxambig", $params_cmd)}
{assign var="maxambig_index" value=$params_cmd|@array_keys:"maxambig"}
<li class="parameter">Discard sequences with more than {$params_cmd[$maxambig_index[0]+1]} ambiguous bases.</li>
{/if}
{if in_array("maxhomop", $params_cmd)}
{assign var="maxhomop_index" value=$params_cmd|@array_keys:"maxhomop"}
<li class="parameter">Clean reads with homopolymers with a size higher than {$params_cmd[$maxhomop_index[0]+1]}.</li>
{/if}
{if in_array("minlength" , $params_cmd)}
{assign var="minlength_index" value=$params_cmd|@array_keys:"minlength"}
<li class="parameter">Clean reads with a length smaller than {$params_cmd[$minlength_index[0]+1]}</li>
{/if}
{if in_array("maxlength" , $params_cmd)}
{assign var="maxlength_index" value=$params_cmd|@array_keys:"maxlength"}
<li class="parameter">Clean reads with a length higher than {$params_cmd[$maxlength_index[0]+1]}</li>
{/if}
{if in_array("pdiffs", $params_cmd)}
{assign var="pdiffs_index" value=$params_cmd|@array_keys:"pdiffs"}
<li class="parameter">The maximum number of differences allowed with the primer is {$params_cmd[$pdiffs_index[0]+1]|replace:')':''}.</li>
{/if}
{/foreach}
<br />
<li class="parameter">{$analyse.params}</li>
</ul>
{/block}
......
......@@ -84,11 +84,11 @@ class MothurTrimSeqs(Analysis):
self.p_trim_stdout = OutputFileList(self.get_outputs('{basename_woext}.primerstrim.stdout', self.fasta_files))
def define_analysis(self):
self.name = "roche 454 cleaning fasta"
self.description = "Cleaning primers."
self.name = "Cleaning"
self.description = "Clean fasta file considering homopolymers, length, ..."
self.software = "mothur"
self.options = "#trim.seqs(fasta=FILE.trim.fasta,name=FILE.trim.names,oligos=primers.oligos,flip="+str(self.flip)+",qaverage="+str(self.qaverage)+",maxambig="+\
str(self.maxambig)+",maxhomop="+str(self.maxhomop)+",minlength="+str(self.minlength)+",maxlength="+str(self.maxlength)+",pdiffs="+str(self.pdiffs)+");"
str(self.maxambig)+",maxhomop="+str(self.maxhomop)+",minlength="+str(self.minlength)+",maxlength="+str(self.maxlength)+",pdiffs="+str(self.pdiffs)+")"
def get_version(self):
cmd = [self.get_exec_path("mothur"), "-version"]
......
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