diff fasta-stats.xml @ 0:9c620a950d3a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ commit d6a78405947a91659a4168ddb2f1534327f044cb
author iuc
date Thu, 22 Nov 2018 04:16:35 -0500
parents
children 16f1f3e2de42
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta-stats.xml	Thu Nov 22 04:16:35 2018 -0500
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+<tool id="fasta-stats" name="Fasta Statistics" version="1.0.1">
+    <description>Display summary statistics for a fasta file.</description>
+    <requirements>
+        <requirement type="package" version="5.26">perl</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        perl '${__tool_directory__}/fasta-stats.pl'
+        '$dataset'
+        > '$stats'
+        ]]>
+    </command>
+    <inputs>
+        <param name="dataset" type="data" format="fasta" label="fasta or multifasta file" help="fasta dataset to get statistics for."/>
+    </inputs>
+    <outputs>
+        <data name="stats" format="tabular" label="${tool.name} on ${on_string}: Fasta summary stats"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="dataset" value="test.fasta"/>
+            <output name="stats" file="test_out.txt"/>
+        </test>
+    </tests>
+    <help>
+**Fasta Stats**
+Displays the summary statistics for a fasta file.
+
+------
+
+Outputs in tabular form:
+    Lengths: n50, min, max, median and average
+
+    Number of base pairs: A, C, G, T, N, Total and Total_not_N
+
+    Number of sequences
+
+    GC content in %
+
+------
+
+Inputs:
+
+Fasta dataset
+    </help>
+    <citations>
+        <citation type="bibtex">
+@UNPUBLISHED{Seemann_Gladman2012,
+    author = {Torsten Seemann and Simon Gladman},
+    title = {Fasta Statistics: Display summary statistics for a fasta file.},
+    year = {2012},
+    url = {https://github.com/galaxyproject/tools-iuc},
+}
+        </citation>
+    </citations>
+</tool>