Mercurial > repos > iuc > poretools_tabular

diff poretools_tabular.xml @ 0:7f0b324de883 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
author iuc
date Tue, 19 Dec 2017 14:56:23 -0500
parents
children 5f5f1da94d7f
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/poretools_tabular.xml	Tue Dec 19 14:56:23 2017 -0500
@@ -0,0 +1,56 @@
+<?xml version="1.0"?>
+<tool id="poretools_tabular" name="Extract FASTQ" version="@VERSION@.0">
+    <description>in tabular format from a set of FAST5 files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="aggressive">
+    <![CDATA[
+        poretools tabular --type $type '$input' > '$output'
+    ]]>
+    </command>
+    <inputs>
+        <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
+        <expand macro="stat_options" />
+    </inputs>
+    <outputs>
+        <data name="output" format="tabular" />
+    </outputs>
+    <tests>
+        <test>
+            <expand macro="test_input" />
+            <param name="types" value="fwd" />
+            <param name="detailed" value="true" />
+            <output name="output" file="poretools-tabular-out1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="types" value="rev" />
+            <param name="detailed" value="false" />
+            <output name="output" file="poretools-tabular-out2.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="types" value="2D" />
+            <param name="detailed" value="true" />
+            <output name="output" file="poretools-tabular-out3.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="types" value="best" />
+            <param name="detailed" value="false" />
+            <output name="output" file="poretools-tabular-out4.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <expand macro="test_input" />
+            <param name="types" value="all" />
+            <param name="detailed" value="true" />
+            <output name="output" file="poretools-tabular-out5.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help>
+        Dump the length, name, sequence, and quality scores of the sequence in one or a set of FAST5 files.
+    </help>
+    <expand macro="citations" />
+</tool>