tools: add 4 little tools

to test remote execution.
to compare remote and local execution.

.gitignore

@@ -55,7 +55,7 @@ tool_shed_wsgi.ini
 
 # Config files.
 datatypes_conf.xml
-tool_conf.xml
+#tool_conf.xml
 external_service_types_conf.xml
 migrated_tools_conf.xml
 shed_tool_conf.xml

config/tool_conf.xml

+<?xml version='1.0' encoding='utf-8'?>
+<toolbox monitor="true">
+  <section id="getext" name="Get Data">
+    <tool file="data_source/upload.xml" />
+    <tool file="data_source/ucsc_tablebrowser.xml" />
+    <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
+    <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/ebi_sra.xml" />
+    <tool file="data_source/fly_modencode.xml" />
+    <tool file="data_source/flymine.xml" />
+    <!-- <tool file="data_source/flymine_test.xml" /> -->
+    <tool file="data_source/modmine.xml" />
+    <tool file="data_source/mousemine.xml" />
+    <tool file="data_source/ratmine.xml" />
+    <tool file="data_source/yeastmine.xml" />
+    <tool file="data_source/worm_modencode.xml" />
+    <tool file="data_source/wormbase.xml" />
+    <!-- <tool file="data_source/wormbase_test.xml" /> -->
+    <tool file="data_source/zebrafishmine.xml" />
+    <tool file="data_source/eupathdb.xml" />
+    <tool file="data_source/hbvar.xml" />
+    <tool file="genomespace/genomespace_importer.xml" />
+    <tool file="genomespace/genomespace_push.xml" />
+  </section>
+  <section id="send" name="Send Data">
+    <tool file="genomespace/genomespace_exporter.xml" />
+  </section>
+  <section id="collection_operations" name="Collection Operations">
+    <tool file="${model_tools_path}/unzip_collection.xml" />
+    <tool file="${model_tools_path}/zip_collection.xml" />
+    <tool file="${model_tools_path}/filter_failed_collection.xml" />
+    <tool file="${model_tools_path}/flatten_collection.xml" />
+    <tool file="${model_tools_path}/merge_collection.xml" />
+    <tool file="${model_tools_path}/relabel_from_file.xml" />
+    <tool file="${model_tools_path}/filter_from_file.xml" />
+    <tool file="${model_tools_path}/sort_collection_list.xml" />
+    <tool file="${model_tools_path}/tag_collection_from_file.xml" />
+    <tool file="${model_tools_path}/apply_rules.xml" />
+  </section>
+  <section id="liftOver" name="Lift-Over">
+    <tool file="extract/liftOver_wrapper.xml" />
+  </section>
+  <section id="textutil" name="Text Manipulation">
+    <tool file="filters/fixedValueColumn.xml" />
+    <tool file="filters/catWrapper.xml" />
+    <tool file="filters/cutWrapper.xml" />
+    <tool file="filters/mergeCols.xml" />
+    <tool file="filters/convert_characters.xml" />
+    <tool file="filters/CreateInterval.xml" />
+    <tool file="filters/cutWrapper.xml" />
+    <tool file="filters/changeCase.xml" />
+    <tool file="filters/pasteWrapper.xml" />
+    <tool file="filters/remove_beginning.xml" />
+    <tool file="filters/randomlines.xml" />
+    <tool file="filters/headWrapper.xml" />
+    <tool file="filters/tailWrapper.xml" />
+    <tool file="filters/trimmer.xml" />
+    <tool file="filters/wc_gnu.xml" />
+    <tool file="filters/secure_hash_message_digest.xml" />
+  </section>
+  <section id="convert" name="Convert Formats">
+    <tool file="filters/bed2gff.xml" />
+    <tool file="filters/gff2bed.xml" />
+    <tool file="maf/maf_to_bed.xml" />
+    <tool file="maf/maf_to_interval.xml" />
+    <tool file="maf/maf_to_fasta.xml" />
+    <tool file="filters/sff_extractor.xml" />
+    <tool file="filters/wig_to_bigwig.xml" />
+    <tool file="filters/bed_to_bigbed.xml" />
+  </section>
+  <section id="filter" name="Filter and Sort">
+    <tool file="stats/filtering.xml" />
+    <tool file="filters/sorter.xml" />
+    <tool file="filters/grep.xml" />
+    <label id="gff" text="GFF" />
+    <tool file="filters/gff/extract_GFF_Features.xml" />
+    <tool file="filters/gff/gff_filter_by_attribute.xml" />
+    <tool file="filters/gff/gff_filter_by_feature_count.xml" />
+    <tool file="filters/gff/gtf_filter_by_attribute_values_list.xml" />
+  </section>
+  <section id="group" name="Join, Subtract and Group">
+    <tool file="filters/joiner.xml" />
+    <tool file="filters/compare.xml" />
+    <tool file="stats/grouping.xml" />
+  </section>
+  <section id="fetchAlignSeq" name="Fetch Alignments/Sequences">
+    <tool file="maf/interval2maf_pairwise.xml" />
+    <tool file="maf/interval2maf.xml" />
+    <tool file="maf/maf_split_by_species.xml" />
+    <tool file="maf/interval_maf_to_merged_fasta.xml" />
+    <tool file="maf/genebed_maf_to_fasta.xml" />
+    <tool file="maf/maf_stats.xml" />
+    <tool file="maf/maf_thread_for_species.xml" />
+    <tool file="maf/maf_limit_to_species.xml" />
+    <tool file="maf/maf_limit_size.xml" />
+    <tool file="maf/maf_by_block_number.xml" />
+    <tool file="maf/maf_reverse_complement.xml" />
+    <tool file="maf/maf_filter.xml" />
+  </section>
+  <section id="bxops" name="Operate on Genomic Intervals" version="">
+    <tool file="filters/wiggle_to_simple.xml" />
+    <tool file="stats/aggregate_binned_scores_in_intervals.xml" />
+    <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
+  </section>
+  <section id="stats" name="Statistics">
+    <tool file="stats/gsummary.xml" />
+    <tool file="filters/uniq.xml" />
+  </section>
+  <section id="plots" name="Graph/Display Data">
+    <tool file="maf/vcf_to_maf_customtrack.xml" />
+  </section>
+  <section id="hgv" name="Phenotype Association">
+    <tool file="evolution/codingSnps.xml" />
+    <tool file="evolution/add_scores.xml" />
+    <tool file="phenotype_association/sift.xml" />
+    <tool file="phenotype_association/linkToGProfile.xml" />
+    <tool file="phenotype_association/linkToDavid.xml" />
+    <tool file="phenotype_association/ldtools.xml" />
+    <tool file="phenotype_association/pass.xml" />
+    <tool file="phenotype_association/gpass.xml" />
+    <tool file="phenotype_association/beam.xml" />
+    <tool file="phenotype_association/lps.xml" />
+    <tool file="phenotype_association/master2pg.xml" />
+  </section>
+  <section id="test" name="Tests">
+    <tool file="runtask/runtask.xml" />
+    <tool file="uname/uname.xml" />
+    <tool file="runtaskloc/runtask.xml" />
+    <tool file="unameloc/uname.xml" />
+  </section>
+</toolbox>

tools/runtask/runtask

+#!/bin/bash
+
+# this script echoes some useful outputs so we can see what parallel
+# and srun are doing
+
+sleepsecs=$[ ( $RANDOM % 10 )  + 10 ]s
+
+# $1 is arg1:{1} from parallel.
+# $PARALLEL_SEQ is a special variable from parallel. It is the actual sequence
+# number of the job regardless of the arguments given
+# We print the sleep time, hostname, and date for more info
+echo task $1 seq:$PARALLEL_SEQ sleep:$sleepsecs host:$(hostname) date:$(date)
+
+# sleep a random amount of time
+sleep $sleepsecs

tools/runtask/runtask.xml

+<tool id="runtask" name="runtask" version="1.0.0">
+	<description>this script echoes some useful outputs so we can see what parallel and srun are doing</description>
+	
+	<command interpreter="bash">
+		runtask singleTask > $output
+	</command>
+	
+	<outputs>
+		<data format="txt" name="output" />
+	</outputs>
+<help>
+
+**What it does**
+
+</help>
+</tool>

tools/runtaskloc/runtask

+#!/bin/bash
+
+# this script echoes some useful outputs so we can see what parallel
+# and srun are doing
+
+sleepsecs=$[ ( $RANDOM % 10 )  + 10 ]s
+
+# $1 is arg1:{1} from parallel.
+# $PARALLEL_SEQ is a special variable from parallel. It is the actual sequence
+# number of the job regardless of the arguments given
+# We print the sleep time, hostname, and date for more info
+echo task $1 seq:$PARALLEL_SEQ sleep:$sleepsecs host:$(hostname) date:$(date)
+
+# sleep a random amount of time
+sleep $sleepsecs

tools/runtaskloc/runtask.xml

+<tool id="runtaskloc" name="runtaskiloc" version="1.0.0">
+	<description>this script echoes some useful outputs so we can see what parallel and srun are doing</description>
+	
+	<command interpreter="bash">
+		runtask singleTask > $output
+	</command>
+	
+	<outputs>
+		<data format="txt" name="output" />
+	</outputs>
+<help>
+
+**What it does**
+
+</help>
+</tool>

tools/uname/uname.xml

+<tool id="uname" name="uname" version="1.0.0">
+	<description>Tell the node running</description>
+	
+	<command>
+   	<![CDATA[
+		uname -a > $output
+ 	]]>
+	</command>
+	
+	<outputs>
+		<data format="txt" name="output" />
+	</outputs>
+<help>
+
+**What it does**
+
+uname -a
+
+</help>
+</tool>

tools/unameloc/uname.xml

+<tool id="unameloc" name="unameloc" version="1.0.0">
+	<description>Tell the node running</description>
+	
+	<command>
+   	<![CDATA[
+		uname -a > $output
+ 	]]>
+	</command>
+	
+	<outputs>
+		<data format="txt" name="output" />
+	</outputs>
+<help>
+
+**What it does**
+
+uname -a
+
+</help>
+</tool>