diff pindel.xml @ 1:374bb08157ca draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 41388a30836a24988ff78645b9446480c1c59990

--- a/pindel.xml	Tue May 17 04:47:23 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,94 +0,0 @@
-<tool id ="pindel" name="Pindel" version="0.2.5b8">
-    <description></description>
-    <requirements>
-        <requirement type="package" version="0.2.5b8">pindel</requirement>
-    </requirements>
-    <stdio>
-        <exit_code range="1:" />
-    </stdio>
-    <command><![CDATA[
-        ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai &&
-        ln -f -s "$input_file" alignment.sorted.bam &&
-        ln -f -s "$reference" ref.fa &&
-        samtools faidx ref.fa &&
-       python $__tool_directory__/create_config_file.py
-        --input_file alignment.sorted.bam
-        --insert_size "$insert_size"
-        --sample_label "$input_file.element_identifier"
-        --output_config_file output_config_file &&
-        pindel
-        -f ref.fa
-        -i output_config_file
-        -c "$chromosome"
-        -o prefix &&
-        mv prefix_D $Deletions &&
-        mv prefix_SI $Short_Insertions &&
-        mv prefix_LI $Long_Insertions &&
-        mv prefix_INV $Inversions &&
-        mv prefix_TD $Tandem_Duplications &&
-        mv prefix_RP $Read_Pair &&
-        mv prefix_INT_final $INT_final &&
-        mv prefix_CloseEndMapped $Close_End_Mapped
-    ]]></command>
-    <inputs>
-        <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/>
-        <param name="insert_size" type="integer" value="" label="Expected Insert size" />
-        <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/>
-        <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes"
-               label="Which chromosome to operate on"/>
-    </inputs>
-    <outputs>
-        <data format="txt" name="Deletions" type="data" label="${input_file.element_identifier} Deletions"/>
-        <data format="txt" name="Short_Insertions" type="data" label="${input_file.element_identifier} Short Insertions"/>
-        <data format="txt" name="Long_Insertions" type="data" label="${input_file.element_identifier} Long Insertions"/>
-        <data format="txt" name="Inversions" type="data" label="${input_file.element_identifier} Inversions"/>
-        <data format="txt" name="Tandem_Duplications" type="data" label="${input_file.element_identifier} Tandom Duplications"/>
-        <data format="txt" name="Breakpoints" type="data" label="${input_file.element_identifier} Breakpoints"/>
-        <data format="txt" name="Read_Pair" type="data" label="${input_file.element_identifier} Read Pair Evidence"/>
-        <data format="txt" name="INT_final" type="data" label="${input_file.element_identifier} INT_final"/>
-        <data format="txt" name="Close_End_Mapped" type="data" label="${input_file.element_identifier} Close End Mapped"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/>
-            <param name="insert_size" value="250"/>
-            <param name="reference" value="dm6.fa" ftype="fasta"/>
-            <param name="chromosome" value="ALL"/>
-            <output name="Deletions" file="X_100000_Hum1.bam_Deletions" ftype="txt"/>
-            <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions" ftype="txt"/>
-            <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions" ftype="txt"/>
-            <output name="Inversions" file="X_100000_Hum1.bam_Inversions" ftype="txt"/>
-            <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications" ftype="txt"/>
-            <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints" ftype="txt"/>
-            <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence" ftype="txt"/>
-            <output name="INT_Final" file="X_100000_Hum1.bam_INT_final" ftype="txt"/>
-            <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped" ftype="txt"/>
-        </test>
-    </tests>
-    <help> <![CDATA[
-
-Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequencing data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
-
-The following inputs/parameters are required:
-- One or more BAM alignment files produced by BWA
-- Expected Insert Size for each alignment file
-- Sample label for each alignment file
-- Reference genome in fasta format (same one used in alignment)
-- Which chromosome to operate on
-
-The following output files are produced by Pindel:
-- Deletions
-- Short Insertions
-- Long Insertions
-- Inversions
-- Tandom Duplications
-- Breakpoints
-- Read Pair Evidence
-- INT_final
-- Close End Mapped
-
-    ]]> </help>
-    <citations>
-        <citation type="doi">doi:10.1093/bioinformatics/btp394</citation>
-    </citations>
-</tool>
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