Mercurial > repos > bgruening > rnaz_annotate

diff rnazAnnotate.xml @ 0:e123d5c6f489 draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty
author bgruening
date Wed, 30 Jan 2019 04:12:06 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazAnnotate.xml	Wed Jan 30 04:12:06 2019 -0500
@@ -0,0 +1,59 @@
+<tool id="rnaz_annotate" name="Annotate RNAz" version="2.1">
+    <requirements>
+        <requirement type="package" version="2.1">rnaz</requirement>
+        <requirement type="package" version="3.6.7">python</requirement>
+        <requirement type="package" version="0.8.0">pybedtools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    python3 '$__tool_directory__/AnnotateRNAz.py'
+    --bed '$bed'
+    --input '$input'
+    --bedout '$output1'
+    --rnazout '$output2'
+    ]]></command>
+    <inputs>
+        <param format="txt" name="input" type="data" label="RNAz output to annotate" />
+        <param type="data" name="bed" format="bed" label="Bed file with annotation" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="bed" />
+        <data name="output2" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="unknown.rnaz.clustered"/>
+            <param name="bed" value="Annotation.bed"/>
+            <output name="output1" file="unknown.rnaz.clustered.annotated.bed"/>
+            <output name="output2" file="unknown.rnaz.clustered.annotated.rnaz"/>
+        </test>
+        <test>
+            <param name="input" value="tRNA.rnaz.clustered"/>
+            <param name="bed" value="Annotation.bed"/>
+            <output name="output1" file="tRNA.rnaz.clustered.annotated.bed"/>
+            <output name="output2" file="tRNA.rnaz.clustered.annotated.rnaz"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    Annotated rnaz hits with an annotation BED file, 
+    replaces rnazAnnotate.pl and rnazIndex.pl.
+    Best used after clustering of RNAz hits.
+
+    usage: AnnotateRNAz.py [-h] [-b BED] [-i INPUT] [-o BEDOUT] [-r RNAZOUT]
+
+    Intersect RNAz output with Annotation from BED
+
+    optional arguments:
+    -h, --help            show this help message and exit
+    -b BED, --bed BED     Annotation BED file
+    -i INPUT, --input INPUT (RNAz output)
+    -o BEDOUT, --bedout BEDOUT (Annotated BED output)
+    -r RNAZOUT, --rnazout RNAZOUT (Annotated rnaz-format output)
+    ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1142/9789814295291_0009</citation>
+    </citations>
+
+</tool>