# HG changeset patch
# User jbrayet
# Date 1448439707 18000
# Node ID fb7fc6b2e74c7f364bf2392d964331e582090e8d
# Parent  27733b98c415450b3abe573a673c1b87cb026a44
Uploaded

diff -r 27733b98c415 -r fb7fc6b2e74c sam_to_bam.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sam_to_bam.xml	Wed Nov 25 03:21:47 2015 -0500
@@ -0,0 +1,89 @@
+<tool id="sam_to_bam" name="SAM-to-BAM" version="2.1">
+  <description>convert SAM to BAM</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></expand>
+  <expand macro="version_command"></expand>
+  <command>
+    <![CDATA[
+        #if $source.index_source == "history":
+          ln -s $source.ref_file input.fa &&
+          samtools faidx input.fa &&
+        #else
+          ln -s ${source.index.fields.path} input.fa &&
+          ln -s ${source.index.fields.path}.fai input.fa.fai &&
+        #end if
+        samtools view -b -@ \${GALAXY_SLOTS:-1} -t input.fa.fai "$input1" | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o "$output1" -T temp
+    ]]>
+    </command>
+    <inputs>
+        <conditional name="source">
+            <param label="Choose the source for the reference genome" name="index_source" type="select">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from the history</option>
+            </param>
+            <when value="cached">
+                <param format="sam" label="SAM file to convert" metadata_name="dbkey" name="input1" type="data">
+                    <validator type="unspecified_build" />
+                    <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
+                </param>
+                <param label="Using reference genome" name="index" type="select">
+                    <options from_data_table="fasta_indexes">
+                        <filter column="1" key="dbkey" ref="input1" type="data_meta" />
+                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param format="sam" label="SAM file to convert" name="input1" type="data" />
+                <param format="fasta" label="Using reference file" metadata_name="dbkey" name="ref_file" type="data" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bam" label="${tool.name} on ${on_string}: converted BAM" name="output1">
+            <actions>
+                <conditional name="source.index_source">
+                    <when value="cached">
+                        <action name="dbkey" type="metadata">
+                            <option name="source.input1" param_attribute="dbkey" type="from_param" />
+                        </action>
+                    </when>
+                    <when value="history">
+                        <action name="dbkey" type="metadata">
+                            <option name="source.ref_file" param_attribute="dbkey" type="from_param" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_in1.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out1.bam" ftype="bam" name="output1" />
+        </test>
+        <test>
+            <param name="index_source" value="history" />
+            <param name="input1" ftype="sam" value="sam_to_bam_noheader_in2.sam" />
+            <param dbkey="equCab2" ftype="fasta" name="ref_file" value="chr_m.fasta" />
+            <output file="sam_to_bam_out3.bam" ftype="bam" name="output1" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Converts SAM dataset into its binary, BAM, representation using ``samtools sort`` and ``view`` commands::
+
+  samtools sort -O bam -o sorted_input.bam [INPUT SAM] 
+  samtools view -b -h -o -T [REFERENCE GENOME] [OUTPUT BAM] sorted_input.bam
+
+]]>
+  </help>
+  <expand macro="citations"></expand>
+</tool>