diff write_supplementary_fastq.xml @ 9:53b71263e2a2 draft

planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 9ff264c527e1fe33950b33f2041c08f6c5758a1e-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/write_supplementary_fastq.xml	Wed Mar 08 05:14:25 2017 -0500
@@ -0,0 +1,37 @@
+<tool id="write_supplementary_fastq" name="Extract supplementary alignments" version="0.3.5">
+    <description>from SAM/BAM alignment files as FASTQ</description>
+    <requirements>
+        <requirement type="package" version="0.3.5">readtagger</requirement>
+    </requirements>
+    <version_command>write_supplementary_fastq --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        write_supplementary_fastq --input_path '$input' --output_path '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" argument="--input_path" type="data" format="bam"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="fastqsanger"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="supplementary.bam" ftype="bam"/>
+            <output name="output" file="supplementary.fastq" ftype="fastqsanger"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. code-block::
+
+    Usage: write_supplementary_fastq [OPTIONS]
+
+      Write all supplementary alignments in `input_path` to an output fastq file
+      at `output_path`.
+
+    Options:
+      --input_path PATH   Collect supplementary reads in this alignment file.
+      --output_path PATH  Write supplementary reads to this FASTQ file.
+      --help              Show this message and exit.
+
+
+    ]]></help>
+</tool>