Mercurial > repos > iuc > seqtk

diff seqtk_telo.xml @ 9:4b494533146a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
author: iuc
date: Sat, 09 Dec 2023 11:14:21 +0000
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqtk_telo.xml	Sat Dec 09 11:14:21 2023 +0000
@@ -0,0 +1,61 @@
+<?xml version="1.0"?>
+<tool id="seqtk_telo" name="seqtk_telo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
+    <description>find telomeres</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+seqtk telo
+-m '$m'
+-p '$p'
+-d '$d'
+-s '$s'
+$P
+'$in_file'
+> '$default'
+    ]]></command>
+    <inputs>
+        <expand macro="in_faq"/>
+        <param argument="-m" type="text" value="CCCTAA" label="Telomere repeat to search for. Default is vertebrate" />
+        <param argument="-p" type="integer" value="1" label="Penalty for a non-repeat" />
+        <param argument="-d" type="integer" value="2000" label="Maximum drop" />
+        <param argument="-s" type="integer" value="300" label="Minimum score" />
+        <param argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="Print scoring" />
+    </inputs>
+    <outputs>
+        <data name="default" format="bed" label="${tool.name} on ${on_string}: telomers"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_file" value="seqtk_telo.fa"/>
+            <output name="default" file="seqtk_telo.out" ftype="bed"/>
+        </test>
+        <test>
+            <param name="in_file" value="seqtk_telo.fa.gz" ftype="fasta.gz"/>
+            <output name="default" file="seqtk_telogz.out" ftype="bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Identifies telomeres using a default vertebrate repeat sequence CCCTAA, or a user supplied one
+
+
+::
+
+     Usage: seqtk telo [options] <in.fq>
+     Options:
+     -m STR     motif [CCCTAA]
+     -p INT     penalty [1]
+     -d INT     max drop [2000]
+     -s INT     min score [300]
+     -P         print scoring
+
+
+@ATTRIBUTION@
+    ]]></help>
+    <expand macro="citation" />
+</tool>