# HG changeset patch
# User trinity_ctat
# Date 1513366562 18000
# Node ID ffa4e316d20a7c752d7a31f769c49f6bc18ad0b1
# Parent  3eba5bd68f0bc42bedb721131071b4ee50d32ef8
Deleted selected files

diff -r 3eba5bd68f0b -r ffa4e316d20a star_fusion.xml
--- a/star_fusion.xml	Fri Dec 15 14:24:50 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<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">
-      <![CDATA[
-      STAR-Fusion
-        --genome_lib_dir "${genome_ref_lib.fields.path}"
-        --left_fq  "${left_input}
-        --right_fq "${right_input}
-        --output_dir subdir
-      ]]>
-    </command>
-    <stdio>
-      <exit_code range="1:"  level="fatal"   description="Error returned from pipeline" />
-    </stdio>
-    <regex match="Must investigate error above."
-           source="stderr"
-           level="fatal"
-           description="Unknown error encountered" />
-    <inputs>
-      <param format="fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
-      <param format="fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
-      <param name="genome_ref_lib" type="select" label="Select a reference genome">
-        <options from_data_table="ctat_genome_ref_libs">
-          <filter type="sort_by" column="2" />
-          <validator type="no_options" message="No indexes are available" />
-        </options>
-      </param>
-
-    </inputs>
-    <outputs>
-      <data format="txt" name="starfusion_log" label="${tool.name} on ${on_string}: log" from_work_dir="subdir/Log.out"/>
-      <data format="bam" name="aligned_bam" label="${tool.name} on ${on_string}: Aligned Bam" from_work_dir="subdir/Aligned.sortedByCoord.out.bam"/>
-      <data format="tabular" name="candidates" label="${tool.name} on ${on_string}: Fusion candidates" from_work_dir="subdir/star-fusion.fusion_candidates.final.abridged"/>
-      <data format="tabular" name="chimeric_junc" label="${tool.name} on ${on_string}: Chimeric.out.junction" from_work_dir="subdir/Chimeric.out.junction"/> 
-    </outputs>
-    <tests>
-      <test>
-        <param name="left_input" value="StarFusion/reads_1.fq.gz" />
-        <param name="right_input" value="StarFusion/reads_2.fq.gz" />
-        <!--
-        <param name="left_input" value="reads.left.simPE.fq" />
-        <param name="right_input" value="reads.right.simPE.fq" />
-        -->
-        <!--
-        <output name="aligned_bam" file="SF_out_aligned.bam" />
-        <output name="candidates" file="SF_out_fusion_candidates.dat" />
-        <output name="chimeric_junc" file="SF_out_chimeric.junction" />
-        <output name="starfusion_log" file="SF_out.log" />
-        -->
-        <output name="starfusion_log">
-            <assert_contents>
-               <has_line_matching expression=".+" />
-               <has_line line="ALL DONE!" />
-            </assert_contents>
-        </output>
-        <output name="aligned_bam">
-            <assert_contents>
-               <has_line_matching expression=".+" />
-               <!-- The following checks for the magic number at the start of the bam file -->
-               <!-- At first I thought "\x8B\x1F" was the number, but it turns out the file
-                    produced by the StarFusion test had that sequence in the file somewhere else.
-               -->
-               <has_text_matching expression="\x1F\x8B" />
-            </assert_contents>
-        </output>
-        <output name="candidates">
-            <assert_contents>
-               <has_line_matching expression=".+" />
-               <has_line line="#fusion_name&#009;JunctionReads&#009;SpanningFrags&#009;Splice_type&#009;LeftGene&#009;LeftBreakpoint&#009;RightGene&#009;RightBreakpoint&#009;Long_double_anchor_support" />
-            </assert_contents>
-        </output>
-        <output name="chimeric_junc">
-            <assert_contents>
-               <has_line_matching expression=".+" />
-               <has_line_matching expression="^chr20.*" />
-            </assert_contents>
-        </output>
-      </test>
-    </tests>
-    <help>
-.. class:: infomark
-
-STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. Please read more here_.
-
-.. _here: https://github.com/STAR-Fusion/STAR-Fusion/wiki
-
-    </help>
-</tool>
diff -r 3eba5bd68f0b -r ffa4e316d20a tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Dec 15 14:24:50 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<tables>
-    <table name="ctat_genome_ref_libs" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, name, path</columns>
-        <file path="tool-data/ctat_genome_ref_libs.loc" />
-    </table>
-</tables>