Mercurial > repos > iuc > data_manager_build_kma_index

diff data_manager/kma_build_index.xml @ 0:889cc43b72d6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kma_index/ commit cf775591e6aa55798abe20c77572761076cc535f"
author: iuc
date: Tue, 18 Feb 2020 16:24:23 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kma_build_index.xml	Tue Feb 18 16:24:23 2020 -0500
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool id="kma_build_index" name="KMA Index Builder" tool_type="manage_data" version="1.2.21+galaxy0" profile="19.01">
+    <description>kma index builder</description>
+    <requirements>
+        <requirement type="package" version="1.2.21">kma</requirement>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <version_command>kma -v</version_command>
+    <command detect_errors="exit_code">
+    <![CDATA[
+        python '${__tool_directory__}/kma_build_index.py'
+          '${out_file}'
+          --k ${k}
+          --k_t ${k_t}
+          --k_i ${k_i}
+	  --ML ${ML}
+	  --ht ${ht}
+	  --hq ${hq}
+          --name '${name}'
+	  '${fasta}'
+    ]]>
+    </command>
+    <inputs>
+        <param name="k" type="integer" value="16" min="8" max="32" label="kmer size used for indexing the database." />
+        <param name="k_t" type="integer" value="16" min="8" max="32" label="kmer size used to identify template candidates when running KMA." />
+        <param name="k_i" type="integer" value="16" min="8" max="32" label="kmer size used when performing alignments between two sequences." />
+        <param name="ML" type="integer" value="16" label="Minimum length of templates" />
+        <param name="ht" type="float" value="1.0" min="0.0" max="1.0" label="Homology template" />
+        <param name="hq" type="float" value="1.0" min="0.0" max="1.0" label="Homology query" />
+	<param name="name" type="text" label="Name for index" />
+	<param name="fasta" type="data" format="fasta" label="Sequence to index (fasta)" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="phiX174.fasta"/>
+            <param name="name" value="index"/>
+            <output name="out_file" value="kma_data_manager.json" compare="sim_size" />
+        </test>
+    </tests>
+    <help>
+    </help>
+    <citations>
+        <citation type="doi">10.1186/s12859-018-2336-6</citation>
+    </citations>
+</tool>