changeset 0:1e495837e8d3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/labels.xml	Sat Aug 02 11:20:30 2014 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0"?>
+<tool name="labels" id="bg_labels" version="1.0.5.0">
+    <description>remapper and annotator of alignments</description>
+    <requirements>
+        <requirement type="package" version="1.0.5">labels</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[
+        pylapels
+            -c "${chrom_list}"
+            $alias
+            $sorted
+            -p \${GALAXY_SLOTS:-4}
+            -q
+            -o $output
+            $input_mod
+            $input_bam
+]]>
+    </command>
+    <inputs>
+        <param name="input_bam" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
+        </param>
+        <param name="input_mod" type="data" format="txt" label="MOD file">
+
+        <param name="alias" optional="true" type="data" format="tabular" label="CSV? file for alias classes of sequence name"/> 
+        <param name="sorted" type="boolean" truevalue="-n" falsevalue="" 
+            label="Sort the output BAM file by read names" help="-n"/>
+        <param name="chrom_list" type="text" value="all" label="Comma-separated list of chromosomes in the output" help="e.g. 1,2,3 (-c)" />
+
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+A remapper and annotator of in silico (pseudo) genome alignments.
+
+ https://code.google.com/p/lapels/
+
+]]>
+</help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Aug 02 11:20:30 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>