changeset 0:35b4ff47bf09 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/suspenders.xml	Sat Aug 02 11:18:24 2014 -0400
@@ -0,0 +1,95 @@
+<?xml version="1.0"?>
+<tool name="suspenders" id="bg_suspenders" version="0.2.5.0">
+    <description>merging of labeled alignments</description>
+    <requirements>
+        <requirement type="package" version="0.2.5">suspenders</requirement>
+        <requirement type="package" version="1.2.1">matplotlib</requirement>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <command>
+<![CDATA[
+        #set $inputs = ""
+        #for $counter, $input_bam in enumerate( $reference_source.input_bams ):
+            ln -s "${input_bam.input_bam}" "${counter}.bam";
+            ln -s "${input_bam.input_bam.metadata.bam_index}" "${counter}.bai";
+            set $inputs += '%s ' % $counter
+        #end for
+
+        pysuspenders
+            $labels
+            $union
+            $quality
+            $pileup
+            $image
+            $mate_all
+            $union_all
+            $random_filter
+            #if $chart:
+                -c $image
+            #end if
+            -p \${GALAXY_SLOTS:-4}
+            $output
+            $inputs
+]]>
+    </command>
+    <inputs>
+        <repeat name="input_bams" title="BAM files" min="2" help="sorted by read name">
+            <param name="input_bam" type="data" format="bam" label="BAM file">
+              <validator type="unspecified_build" />
+              <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+            </param>
+        </repeat>
+
+        <param name="labels" type="boolean" truevalue="--lapels" falsevalue="--normal-input"
+            checked="True"
+            label="Input has lapels tags" help="--lapels/--normal-input" />
+
+        <param name="union" type="boolean" truevalue="--union" falsevalue="" 
+            label="Merge the files using the union filter" help="--union"/>
+
+        <param name="quality" type="boolean" truevalue="--quality" falsevalue=""
+            checked="True" label="Merge the files using the quality filter" help="--quality"/>
+
+        <param name="pileup" type="boolean" truevalue="--pileup" falsevalue=""
+            label="merge the files using the quality filter, then the pileup height filter" help="--pileup"/>
+
+        <param name="chart" type="boolean" truevalue="True" falsevalue="False"
+            label="save pileup chart to an image" help=""/>
+
+        <param name="mate_all" type="boolean" truevalue="--mate-all" falsevalue=""
+            label="compare unmated segments to mated ones" help="--mate-all"/>
+
+        <param name="union_all" type="boolean" truevalue="--union-all" falsevalue=""
+            label="Use union filter if other filters fail" help="always active for --union (--union-all)"/>
+
+        <param name="random_filter" type="boolean" truevalue="--random-filer" falsevalue=""
+            label="Use random filter if other filters fail" help="default for --quality and --pileup (--random-filter)"/>
+
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} on ${on_string}"/>
+        <data name="image" format="png" label="${tool.name} on ${on_string}: Chart">
+            <filter>chart is True</filter>
+        <data>
+    </outputs>
+    <tests>
+
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Allows the merging of alignments that have been annotated using pylapels into a single alignment that picks the highest quality alignment.
+
+https://pypi.python.org/pypi/suspenders/
+
+]]>
+</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Aug 02 11:18:24 2014 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="suspenders" version="0.2.5">
+        <repository changeset_revision="b4eeeb49c332" name="package_suspenders_0_2_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>