# HG changeset patch
# User trinity_ctat
# Date 1513365509 18000
# Node ID f90885dda34c86577012b63e334978e2f81e8f74
# Parent  0c6f8f4e77336eea88df434e2b43d6ca860169fa
Adding star_fusion tool.

diff -r 0c6f8f4e7733 -r f90885dda34c star_fusion.xml
--- a/star_fusion.xml	Fri Dec 15 14:12:30 2017 -0500
+++ b/star_fusion.xml	Fri Dec 15 14:18:29 2017 -0500
@@ -1,14 +1,16 @@
-<tool id="star-fusion" name="Star Fusion" version="1.0.0" profile="17.05">
+<tool id="star_fusion" name="Star Fusion" version="1.0.0" profile="17.05">
     <description>Fusion-finding Pipeline Using the STAR Aligner</description>
     <requirements>
 	<requirement type="package" version="1.1.0">star-fusion</requirement>
     </requirements>
     <command detect_errors="default">
-    STAR-Fusion
-    --genome_lib_dir "${genome_ref_lib.fields.path}"
-    --left_fq  "${left_input}
-    --right_fq "${right_input}
-    --output_dir subdir
+      <![CDATA[
+      STAR-Fusion
+        --genome_lib_dir "${genome_ref_lib.fields.path}"
+        --left_fq  "${left_input}
+        --right_fq "${right_input}
+        --output_dir subdir
+      ]]>
     </command>
     <stdio>
       <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
diff -r 0c6f8f4e7733 -r f90885dda34c trinity.xml
--- a/trinity.xml	Fri Dec 15 14:12:30 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,148 +0,0 @@
-<tool id="trinityrnaseq" name="trinity" version="1.0.0" profile="17.05">
-  
-    <!-- Original tool written by Jeremy Goecks,
-        later development/maintenance by (in chronological order)
-            Brian Haas, Ben Fulton, Cicada Dennis 
-    -->
-    <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description>
-    <requirements>
-        <requirement type="package" version="2.7">python</requirement>
-        <requirement type="package">subprocess32</requirement>
-        <requirement type="package">samtools</requirement>
-        <requirement type="package">bzip2</requirement>
-        <requirement type="package" version="2.4.0">trinity</requirement>
-    </requirements>
-    <command detect_errors="default">
-      <![CDATA[
-      python $__tool_directory__/trinity_wrapper.py 
-      --CPU \${GALAXY_SLOTS:-4}
-      --max_memory \${TRINITY_MAX_MEMORY:-31G}
-      #if str($inputs.paired_or_single) == "paired":
-       --left $inputs.left_input --right $inputs.right_input
-       #if $inputs.left_input.ext == 'fasta':
-        --seqType fa
-       #else:
-        --seqType fq
-       #end if
-      #else:
-       --single $inputs.input
-       #if $inputs.input.ext == 'fasta':
-        --seqType fa
-       #else:
-        --seqType fq
-       #end if
-      #end if
-      ## direct to output
-      --timing trinity_out_dir/Trinity.timing
-      --log $trinity_log
-
- ]]>
-      <!-- The fullpath, dir, and user options (preceed with dashes) can be
-           used in the trinity_wrapper.py command to create rerunable jobs.
-           We are not supporting rerunable jobs in this release of this tool.
-        fullpath \${TRINITY_RERUN_PREFIX}
-        dir '$adv.rerundir'
-        user $__user_id__
-      mem_per_cpu 31
-      -->
-    </command>
-    <stdio>
-      <exit_code range="1:"   level="fatal"   description="Program failed" />
-      <exit_code range=":-1"   level="fatal"   description="DRM killed job" />
-    </stdio>
-    <inputs>
-      <conditional name="inputs">
-	<param name="paired_or_single" type="select" label="Paired or Single-end data?">
-          <option value="paired">Paired</option>
-          <option value="single">Single</option>
-        </param>
-        <when value="paired">
-          <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-          <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
-        </when>
-        <when value="single">
-          <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
-        </when>
-      </conditional>
-      <!-- The following section was used to aid in creating rerunable jobs.
-           We are not supporting rerunable jobs in this release of this tool.
-      <section name="adv" title="Allow Job Rerun" expanded="False">
-        <param name="rerundir" type="text" size="10" label="To make a job rerunnable, you will need to specify a unique tag to label the job, with no spaces or wierd characters." />
-      </section>
-      -->
-    </inputs>
-    <outputs>
-      <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
-      <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
-    </outputs>
-    <tests>
-            <!-- Not testing with the following inputs anymore.
-            <param name="left_input" value="FLI1.left.fq" />
-            <param name="right_input" value="FLI1.right.fq" />
-            -->
-        <test>
-	    <param name="paired_or_single" value="paired" />
-            <param name="left_input" value="reads.left.simPE.fq" />
-            <param name="right_input" value="reads.right.simPE.fq" />
-            <param name="adv.rerundir" value="planemo_test_1" />
-	    <output name="trinity_log" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line line="Trinity exited with status 0" />
-                </assert_contents>
-            </output>
-	    <output name="assembled_transcripts" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-  	    <param name="paired_or_single" value="paired" />
-            <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
-            <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
-            <param name="adv.rerundir" value="planemo_test_2" />
-            <!-- Following parameters are not used in this version of this tool. -->
-            <!--
-            <param name="JM" value="50G" />
-            <param name="CPU" value="2" />
-            <param name="library_type" value="None" />
-            <param name="group_pairs_distance" value="500" />
-            <param name="path_reinforcement_distance" value="75" />
-            <param name="use_additional" value="no" />
-            -->
-  	    <output name="trinity_log" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line line="Trinity exited with status 0" />
-                </assert_contents>
-            </output>
-  	    <output name="assembled_transcripts" >
-                <assert_contents>
-                    <has_line_matching expression=".+" />
-                    <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-    <help>
-This instance is running Trinity version 2.4.0 and uses the following command:
-
-	 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
-
-Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
-
-.. class:: infomark
-
-Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_.
-
-.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
-.. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
-    </help>
-
-        <citations>
-            <citation type="doi">10.1038/nbt.1883</citation>
-        </citations>
-
-</tool>