diff rnazSelectSeqs.xml @ 0:273a961d332f draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_team/rnaz commit d261ddb93500e1ea309845fa3989c87c6312583d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rnazSelectSeqs.xml	Wed Jan 30 04:13:47 2019 -0500
@@ -0,0 +1,85 @@
+<tool id="rnaz_select_seqs" name="RNAz Select Seqs" version="2.1">
+    <requirements>
+        <requirement type="package" version="2.1">rnaz</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    rnazSelectSeqs.pl
+        --num-seqs $numseqs
+        --num-samples $numsamples
+        --opt-id $optid
+        --max-id $maxid
+        #if $noref:
+            --no-ref $noref
+        #end if
+        '$input'
+    > '$output'
+    ]]></command>
+    <inputs>
+        <param format="txt" name="input" type="data" label="Input Alignment File" />
+        <param argument="--num-seqs" name="numseqs" type="integer" value="6" label="Number of sequences in the output alignment(s). (Default:6)" />
+        <param argument="--num-samples" name="numsamples" type="integer" value="1" label="Number of output alignments (Default: 1)" />
+        <param argument="--opt-id" name="optid" type="integer" value="80"
+            label="The resulting alignment(s) is (are) optimized for this value of mean pairwise identity (in percent, default: 80)" />
+        <param argument="--max-id" name="maxid" type="integer" value="99"
+            label="Sequences from pairs with pairwise identity higher than X% are removed (default: 99, i.e. only almost identical sequences areremoved)" />
+        <param argument="--no-reference" name="noref" type="boolean" checked="false" truevalue="--no-reference" falsevalue=""
+            label="By default the first sequence (=reference sequence) is always present in the output alignment(s). If you do not care having it removed, set this flag." />
+    </inputs>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="tRNA.aln"/>
+            <param name="numseqs" value="1"/>
+            <output name="output" file="tRNA_selected.aln"/>
+        </test>
+    </tests>
+    <help><![CDATA[ RNAz up to version 1.0 was limited to alignments
+    of at most 6 sequences.  As of version 2.0, there is no limit on
+    the maximum number of sequences.  However, under some cirumstances
+    (e.g. for very large alignments) it is still useful to reduce the
+    number of sequences prior to running RNAz.  You can select an
+    optimal subset of sequences using rnazSelectSeqs.pl before you
+    put it into RNAz:
+
+    Usage:
+    rnazSelectSeqs.pl [options] [file]
+
+    Options:
+    -n N, --num-seqs=N
+    Number of sequences in the output alignment(s). (Default:6)
+
+    -a N, --num-samples=N
+    Number of output alignments (Default: 1)
+
+    -i X, --opt-id=X
+    The resulting alignment(s) is (are) optimized for this value of
+    mean pairwise identity (in percent, default: 80)
+
+    --max-id=X
+    Sequences from pairs with pairwise identity higher than X% are
+    removed (default: 99, i.e. only almost identical sequences are
+    removed)
+
+    -x, --no-reference
+    By default the first sequence (=reference sequence) is always
+    present in the output alignment(s). If you do not care having it
+    removed, set this flag.
+
+    -v, --version
+    Prints version information and exits.
+
+    -h, --help
+    Prints a short help message and exits.
+
+    --man   Prints a detailed manual page and exits.
+
+
+    ]]></help>
+
+    <citations>
+        <citation type="doi">10.1142/9789814295291_0009</citation>
+    </citations>    
+
+</tool>