diff emboss_degapseq.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68

--- a/emboss_degapseq.xml	Fri Aug 12 19:17:10 2016 -0400
+++ b/emboss_degapseq.xml	Mon Jan 30 13:27:40 2017 -0500
@@ -1,46 +1,47 @@
-<tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
-  <description>Removes gap characters from sequences</description>
-  <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
-  <command>degapseq -sequence $input1 -outseq $out_file1 -osformat2 $out_format1 -auto</command>
-  <inputs>
-    <param format="data" name="input1" type="data">
-      <label>On query</label>
-    </param>
-    <param name="out_format1" type="select">
-      <label>Output Sequence File Format</label>
-      <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>
-  </inputs>
-  <outputs>
-    <data format="fasta" name="out_file1" />
+<tool id="EMBOSS: degapseq20" name="degapseq" version="5.0.0">
+  <description>Removes gap characters from sequences</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <code file="emboss_format_corrector.py" />
+  <command>degapseq -sequence '$input1' -outseq '$out_file1' -osformat2 $out_format1 -auto</command>
+  <inputs>
+    <param name="input1" type="data" format="data" label="On query" />
+    <param name="out_format1" 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>
+  </inputs>
+  <outputs>
+    <data name="out_file1" format="fasta" />
   </outputs>
   <tests>
     <test>
@@ -48,19 +49,11 @@
       <param name="out_format1" value="fasta"/>
       <output name="out_file1" file="emboss_degapseq_out.fasta"/>
     </test>
-  </tests>
-  <code file="emboss_format_corrector.py" />
+  </tests>
   <help>
     You can view the original documentation here_.
-    
-    .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/degapseq.html
-
-------
-
-**Citation**
 
-For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
-
-If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
+    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/degapseq.html
   </help>
-</tool>
\ No newline at end of file
+  <expand macro="citations" />
+</tool>