diff samtools_split_by_chrom.xml @ 0:a30dd3c77b30 draft

planemo upload commit 7491208ca0c917a053798a48c3e54c3e30e95d92

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_split_by_chrom.xml	Wed Nov 30 16:46:40 2016 -0500
@@ -0,0 +1,61 @@
+<tool id="samtools_split_by_chrom" name="Split BAM by Chromosome" version="2.0">
+  <description>into collection</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <!-- <code file="samtools_slice_options.py"/> -->
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+    <command>
+<![CDATA[
+    mkdir -p outputs &&
+    ln -s "${input_bam}" temp_input.bam &&
+    ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai 
+    #for $ref in str( $refs ).split(","):
+        && samtools view -@ \${GALAXY_SLOTS:-1} -bh inputs/temp_input.bam ${ref} |  
+        samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "outputs/${input_bam.name}.${ref}.bam" - 
+    #end for
+]]>
+    </command>
+    <inputs>
+        <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" />
+        <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If &quot;No options available&quot; is displayed, you need to re-detect metadata on the input dataset. See help section below.">
+            <!-- The options tagset below extracts reference names from bam file metadata -->
+            <!-- This will not work with bed files with old style metadata. However this  -->
+            <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
+            <!-- The pencil icon and settind datatype to "bam"                            -->
+            <!-- This change has been commited in the following pull request:             -->
+            <!-- https://github.com/galaxyproject/galaxy/pull/107                         -->
+            <options>
+                <filter type="data_meta" ref="input_bam" key="reference_names" />
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="output_collection" type='list' label="${input_bam.name} by chrom">
+          <discover_datasets pattern="(?P&lt;designation&gt;.+)\.bam" directory="outputs" ext='bam'/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
+            <param name="refs" value="chrM" />
+            <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+Creates a dataset collection of BAM files, one per selected chromosome.
+
+This tool is based on ``samtools view`` command. 
+
+@no-chrom-options@
+
+]]>
+  </help>
+    <expand macro="citations"></expand>
+</tool>