Mercurial > repos > thanhlv > biotradis

diff biotradis_plot.xml @ 0:afe9a515d145 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author thanhlv
date Thu, 25 Jul 2019 06:03:12 -0400
parents
children 09c1f97a5bcc
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/biotradis_plot.xml	Thu Jul 25 06:03:12 2019 -0400
@@ -0,0 +1,34 @@
+<tool id="add_tradis_tags" name="add tradis tags" version="@VERSION@">
+    <description>Create insertion site plot for Artemis</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+    
+    tradis_plot -b $input_bam -m $mapping_quality
+
+    ]]></command>
+    <inputs>
+         <param name="input_bam" type="data" format="bam" label="BAM file" help="" />
+         <param name="mapping_quality" type="integer" value="30" label="mapping quality must be greater than X " help="(optional. default: 30)" />
+    </inputs>
+
+    <outputs>
+       <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="added.tr.bam" />
+    </outputs>
+
+    <tests>
+    </tests>
+    <help><![CDATA[
+        Adds transposon sequence and quality tags to the read strings and
+        outputs a BAM.
+
+        Usage: add_tags -b file.bam [options]
+
+        Options:
+        -b  : bam file with tradis tags
+        -v  : verbose debugging output
+    ]]></help>
+
+</tool>