diff defuse.xml @ 44:225750bf3770 draft

Uploaded

--- a/defuse.xml	Wed May 06 14:31:57 2015 -0500
+++ b/defuse.xml	Mon Jan 04 15:55:00 2016 -0500
@@ -1,12 +1,13 @@
-<tool id="defuse" name="DeFuse" version="1.6.1">
- <description>identify fusion transcripts</description>
- <requirements>
-  <requirement type="package" version="0.6.1">defuse</requirement>
-  <requirement type="package" version="0.1.19">samtools</requirement>
-  <requirement type="package" version="1.0.0">bowtie</requirement>
-  <requirement type="package" version="2013-05-09">gmap</requirement>
-  <requirement type="package" version="latest">kent</requirement>
- </requirements>
+<tool id="defuse" name="DeFuse" version="@DEFUSE_VERSION@.1">
+    <description>identify fusion transcripts</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="defuse_requirement" />
+        <expand macro="mapping_requirements" />
+        <expand macro="r_requirements" />
+    </requirements>
   <command interpreter="command"> /bin/bash $shscript </command>
  <inputs>
   <param name="left_pairendreads" type="data" format="fastq" label="left part of read pairs" help="The left and right reads pairs must be in the same order, and not have any unpaired reads.  (FASTQ interlacer will pair reads and remove the unpaired.   FASTQ de-interlacer will separate the result into left and right reads.)"/>
@@ -79,7 +80,7 @@
   <param name="keep_output" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Save DeFuse working directory files" 
          help="The defuse output working directory can be helpful for determining errors that may have occurred during the run, 
                but they require considerable diskspace, and should be deleted and purged when no longer needed."/>
-  <param name="do_get_reads" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
+  <param name="do_get_reads" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Run get_reads on each cluster"/>
  </inputs>
  <stdio>
    <exit_code range="1:"  level="fatal" description="Error Running Defuse" />
@@ -570,8 +571,10 @@
 cp $defuse_config $config_txt
 ## make a data_dir  and ln -s the input fastq
 mkdir -p data_dir
-ln -s $left_pairendreads data_dir/reads_1.fastq
-ln -s $right_pairendreads data_dir/reads_2.fastq
+## ln -s "$left_pairendreads" data_dir/reads_1.fastq
+## ln -s "$right_pairendreads" data_dir/reads_2.fastq
+cp "$left_pairendreads" data_dir/reads_1.fastq
+cp "$right_pairendreads" data_dir/reads_2.fastq
 ## ln to output_dir in from_work_dir
 #if $defuse_out.__str__ != 'None':
 mkdir -p $defuse_out.dataset.extra_files_path
@@ -580,7 +583,7 @@
 mkdir -p output_dir
 #end if
 ## run defuse.pl
-perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p 8
+perl \${DEFUSE_PATH}/scripts/defuse.pl -name "$library_name" -c $defuse_config -1 data_dir/reads_1.fastq -2 data_dir/reads_2.fastq -o output_dir  -p \$GALAXY_SLOTS
 ## copy primary results to output datasets
 if [ -e output_dir/log/defuse.log ]; then cp output_dir/log/defuse.log $defuse_log; fi
 ## if [ -e output_dir/results.tsv ]; then cp output_dir/results.tsv $results_tsv; fi
@@ -746,4 +749,5 @@
   3596	TGGGGGTTGAGGCTTCTGTTCCCAGGTTCCATGACCTCAGAGGTGGCTGGTGAGGTTATGACCTTTGCCCTCCAGCCCTGGCTTAAAACCTCAGCCCTAGGACCTGGTTAAAGGAAGGGGAGATGGAGCTTTGCCCCGACCCCCCCCCGTTCCCCTCACCTGTCAGCCCGAGCTGGGCCAGGGCCCCTAGGTGGGGAACTGGGCCGGGGGGCGGGCACAAGCGGAGGTGGTGCCCCCAAAAGGGCTCCCGGTGGGGTCTTGCTGAGAAGGTGAGGGGTTCCCGGGGCCGCAGCAGGTGGTGGTGGAGGAGCCAAGCGGCTGTAGAGCAAGGGGTGAGCAGGTTCCAGACCGTAGAGGCGGGCAGCGGCCACGGCCCCGGGTCCAGTTAGCTCCTCACCCGCCTCATAGAAGCGGGGTGGCCTTGCCAGGCGTGGGGGTGCTGCC|TTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATCGAACCCTGATTCCCCGTCACCCGTGGTCACCATGGTAGGCACGGCGACTACCATCGAAAGTTGATAGGGCAGACGTTCGAATGGGTCGTCGCCGCCACGGGGGGCGTGCGATCAGCCCGAGGTTATCTAGAGTCACCAAAGCCGCCGGCGCCCGCCCCCCGGCCGGGGCCGGAGAGGGGCTGACCGGGTTGGTTTTGATCTGATAAATGCACGCATCCCCCCCGCGAAGGGGGTCAGCGCCCGTCGGCATGTATTAGCTCTAGAATTACCACAGTTATCCAAGTAGGAGAGGAGCGAGCGACCAAAGGAACCATAACTGATTTAATGAGCCATTCGCAGTTTCACTGTACCGGCCGTGCGTACTTAGACATGCATGGCTTAATCTTTGAGACAAGCATATGCTACTGGCAGG	250	7.00711162298275e-72	0.00912124762512338	0.00684237452309549	N	N	3.31745197152461	3.47233119514066	3.31745197152461	splitr	7	0.0157657657657656	0	0	N	0.0135135135135136	N	N	0	0	ENSG00000156860	ENSG00000212932	-	+	16	21	30682131	48111157	coding	upstream	FBRS	RPL23AP4	30670289	48110676	+	+	0.0157657657657656	30680678	9827473	-	+	Y	-	-	N	output_dir	2	1	1.11111111111111	1	1	1	N	N	0	1	9	0.325530693397641	0.296465452915709	0.325530693397641	0.296465452915709	2	-	-	
 
  </help>
+    <expand macro="citations"/>
 </tool>