diff shear_sv.xml @ 0:ea76da1e7281

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shear_sv.xml	Fri Jul 05 15:22:04 2013 -0400
@@ -0,0 +1,88 @@
+<?xml version="1.0"?>
+<tool id="shear_sv" name="SHEAR-SV" version="0.0.1">
+  <description>find SVs and estimate the heterogeneity levels from a BAM</description>
+  <requirements>
+    <requirement type="package" version="0.1.2">shear</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+    <requirement type="package" version="0.6.2">bwa</requirement>
+    <requirement type="package" version="1.0.1">crest</requirement>
+    <requirement type="package" version="latest">kent</requirement>
+  </requirements>
+  <!--
+  <version_command></version_command>
+  -->
+  <command>java -jar  \$SHEAR_JAR_PATH/SHEAR.jar sv -r $prefix 
+     -b $bamfile 
+     #if $genomeSource.refGenomeSource == 'indexed':
+       -f $genomeSource.ref_fastas.fields.path 
+       -i $genomeSource.bwa_indices.fields.path 
+       -t $genomeSource.twobit_indice.fields.paths
+     #else:
+       -f $genomeSource.ref_fasta
+       -i $genomeSource.bwa_index
+       -t $genomeSource.twobit
+     #end if
+  </command>
+  <inputs>
+    <param name="bamfile" type="data" format="bam" label="BAM alignment file containing the input sequences to the assembly."/> 
+    <!-- reference data -->
+    <conditional name="genomeSource">
+      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a cached file?">
+        <option value="indexed" selected="true">Use a cached reference genome</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="ref_fastas" type="select" label="Select a reference genome">
+          <options from_data_table="all_fasta">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No reference fasta files are available" />
+          </options>
+        </param>
+        <param name="twobit_indices" type="select" label="Select a reference genome">
+          <options from_data_table="twobit">
+            <filter type="sort_by" column="0" />
+            <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+        <param name="bwa_indices" type="select" label="Select a reference genome">
+          <options from_data_table="bwa_indexes">
+            <filter type="sort_by" column="2" />
+            <filter type="data_meta" ref="ref_fastas" key="dbkey" column="0" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ref_fasta" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+        <param name="twobit" type="data" format="twobit" metadata_name="dbkey" label="Select a reference from history" />
+        <param name="bwa_index" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
+      </when>
+    </conditional>
+    <param name="prefix" type="hidden" value="shear_sv" label="Prefix for all generated files"/>
+  </inputs>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <outputs>
+    <data format="shear.sdi" name="sdi" label="${tool.name} on ${on_string}: shear_sv.sdi" from_work_dir="shear_sv.sdi" />
+    <data format="txt" name="report" label="${tool.name} on ${on_string}: shear_sv.report" from_work_dir="shear_sv.report"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="bamfile" ftype="bam" value="simulated-data.bam"/>
+      <param name="refGenomeSource" value="history"/>
+      <param name="ref_fasta" ftype="fasta" value="syn.fa"/>
+      <param name="bwa_index" ftype="" value="syn.fa"/>
+      <param name="twobit" ftype="twobit" value="syn.2bit"/>
+      <output name="shear.sdi"  file="shear_sv.sdi"/>
+      <output name="report"  file="shear_sv.report"/>
+    </test>
+  </tests>
+  <help>
+SHEAR-SV will process a BAM alignment file to find SVs and estimate the
+heterogeneity level of those SVs. It will output a *.report file reporing the
+SVs and their heterogeneity levels, and it will output a *.sdi file that can be
+used for SHEAR-Assemble to reconstruct the new genome.
+  </help>
+</tool>