diff emboss_checktrans.xml @ 10:d49956b87f7e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/emboss_checktrans.xml	Wed Feb 08 12:42:22 2017 -0500
@@ -0,0 +1,82 @@
+<tool id="EMBOSS: checktrans9" name="checktrans" version="5.0.0.1">
+  <description>Reports STOP codons and ORF statistics of a protein</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>checktrans -sequence '$input1' -outfile '$out_file1' -outseq '$out_file2' -osformat3 $out_format2 -outfeat '$out_file3' -offormat4 $out_format3 -orfml $orfml -addlast $addlast -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="fasta" label="On query" />
+    <param name="orfml" type="integer" value="100" label="Minimum ORF length to report" />
+    <param name="addlast" type="select" label="An asterisk in the protein sequence indicates the position of a STOP codon" help="Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs">
+      <option value="yes">Yes</option>
+      <option value="no">No</option>
+    </param>
+    <param name="out_format2" type="select" label="Output sequence file format">
+      <option value="fasta">FASTA (m)</option>
+      <option value="acedb">ACeDB (m)</option>
+      <option value="asn1">ASN.1 (m)</option>
+      <option value="clustal">Clustal (m)</option>
+      <option value="codata">CODATA (m)</option>
+      <option value="embl">EMBL (m)</option>
+      <option value="fitch">Fitch (m)</option>
+      <option value="gcg">Wisconsin Package GCG 9.x and 10.x (s)</option>
+      <option value="genbank">GENBANK (m)</option>
+      <option value="gff">GFF (m)</option>
+      <option value="hennig86">Hennig86 (m)</option>
+      <option value="ig">Intelligenetics (m)</option>
+      <option value="jackknifer">Jackknifer (m)</option>
+      <option value="jackknifernon">Jackknifernon (m)</option>
+      <option value="mega">Mega (m)</option>
+      <option value="meganon">Meganon (m)</option>
+      <option value="msf">Wisconsin Package GCG's MSF (m)</option>
+      <option value="pir">NBRF (PIR) (m)</option>
+      <option value="ncbi">NCBI style FASTA (m)</option>
+      <option value="nexus">Nexus/PAUP (m)</option>
+      <option value="nexusnon">Nexusnon/PAUPnon (m)</option>
+      <option value="phylip">PHYLIP interleaved (m)</option>
+      <option value="phylipnon">PHYLIP non-interleaved (m)</option>
+      <option value="selex">SELEX (m)</option>
+      <option value="staden">Staden (s)</option>
+      <option value="strider">DNA strider (m)</option>
+      <option value="swiss">SwisProt entry (m)</option>
+      <option value="text">Plain sequence (s)</option>
+      <option value="treecon">Treecon (m)</option>
+    </param>
+    <param name="out_format3" type="select" label="Output feature file format">
+      <option value="gff">GFF</option>
+      <option value="embl">EMBL</option>
+      <option value="swiss">SwissProt</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="checktrans" />
+    <data name="out_file2" format="fasta" />
+    <data name="out_file3" format="gff" />
+  </outputs>
+ <!--   <tests>
+    <test>
+      <param name="input1" value="2.fasta"/>
+      <param name="orfml" value="100"/>
+      <param name="addlast" value="yes"/>
+      <param name="out_format2" value="fasta"/>
+      <param name="out_format3" value="gff"/>
+      <output name="out_file1" file="emboss_checktrans_out1.txt"/>
+      <output name="out_file2" file="emboss_checktrans_out2.fasta"/>
+      <output name="out_file3" file="emboss_checktrans_out3.gff"/>
+    </test>
+  </tests> -->
+  <help>
+.. class:: warningmark
+
+The input dataset needs to be sequences.
+
+-----
+
+    You can view the original documentation here_.
+
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/checktrans.html
+  </help>
+  <expand macro="citations" />
+</tool>