diff pipelign.xml @ 0:cd9d1eccda7e draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pipelign commit 94da3b18b4725a93d8c52469ae809e692ba0cd77"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pipelign.xml	Fri Aug 23 14:47:13 2019 -0400
@@ -0,0 +1,87 @@
+<?xml version="1.0"?>
+<tool id="pipelign" name="Automated multiple sequence" version="@VERSION@+galaxy0">
+    <description>alignment with pipelign</description>
+    <macros>
+        <token name="@VERSION@">0.2</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">pipelign</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        pipelign
+            --outDir files
+            --clearExistingDirectory
+            --inFile '$inFile'
+            --outFile '$outFile'
+            --lenThr $lenThr
+            --alphabet $alphabet
+            --simPer $simPer
+            --merge $merge
+            --thread \${GALAXY_SLOTS:-1}
+            --mIterateLong $mIterateLong
+            --mIterateMerge $mIterateMerge
+            --ambigPer $ambigPer
+            $keepOrphans $keepBadSeqs $excludeClusters
+    ]]></command>
+    <inputs>
+        <param argument="--inFile" type="data" format="fasta" label="Input sequence file" />
+        <param argument="--lenThr" type="float" value="0.7" min="0" max="1" label="Length threshold for full sequences" help="Default: 0.7" />
+        <param argument="--alphabet" type="select" label="Alphabet for input sequences">
+            <option value="dna">DNA</option>
+            <option value="rna">RNA</option>
+            <option value="aa">Amino Acids</option>
+        </param>
+        <param argument="--keepOrphans" type="boolean" truevalue="--keepOrphans" falsevalue="" label="Add fragments without clusters" />
+        <param argument="--keepBadSeqs" type="boolean" truevalue="--keepBadSeqs" falsevalue="" label="Add long sequences with too many ambiguous residues" />
+        <param argument="--simPer" type="float" value="0.8" min="0" max="1" label="Percent sequence similarity for clustering" />
+        <param argument="--merge" type="select" label="Merge strategy">
+            <option value="P">Parallel</option>
+            <option value="C">Consensus</option>
+        </param>
+        <param argument="--mIterateLong" type="integer" value="1" min="1" label="Number of iterations to refine long alignments" />
+        <param argument="--mIterateMerge" type="integer" value="1" min="1" label="Number of iterations to refine merged alignment" />
+        <param argument="--ambigPer" type="float" value="0.1" min="0" max="1" label="Percent sequence similarity for clustering" />
+        <param argument="--excludeClusters" type="boolean" truevalue="--excludeClusters" falsevalue="" label="Exclude clusters from final alignment" />
+    </inputs>
+    <outputs>
+        <data name="outFile" format="fasta" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="inFile" value="pipelign-in1.fasta" />
+            <output name="outFile">
+                <assert_contents>
+                    <has_line line="&gt;K03455|HIVHXB2CG_1739_2301_2_0_0_2_0_0_33/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_5108_5621_3_0_0_2_0_0_23/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_1835_2322_3_0_0_1_0_0_57/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_2276_2810_0_0_0_0_0_0_58/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_2252_2786_0_0_0_0_0_0_c/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_7972_8486_1_0_0_0_0_0_e/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_756_1235_2_0_0_1_0_0_34/1" />
+                    <has_line line="&gt;K03455|HIVHXB2CG_1286_1769_0_0_0_4_0_0_0/1" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+-------------------
+
+A pipeline for automated multiple sequence alignment, particularly of viral sequences.
+
+]]>
+    </help>
+    <citations>
+        <citation type="bibtex">
+            @UNPUBLISHED{spond,
+                author = "A.S.Md.M. Hossain, S.D.W.Frost",
+                title = "Pipelign: an alignment pipeline for viral sequences.",
+                year = "2019",
+                note = "https://github.com/asmmhossain/pipelign/",
+                url = "https://github.com/asmmhossain/pipelign/"}
+        </citation>
+    </citations>
+</tool>