changeset 13:d5c3794bd246 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit ca9a6baaede679d619675e48d665748a91950115
author iuc
date Mon, 23 Apr 2018 13:04:47 -0400
parents ace31bbde4c0
children 27c43fb015f0
files emboss_iep.xml emboss_tranalign.xml emboss_transeq.xml test-data/emboss_cai_out.cai test-data/emboss_newcpgseek_out.newcpgseek test-data/emboss_tranalign_out.fasta
diffstat 6 files changed, 211 insertions(+), 204 deletions(-) [+]
line wrap: on
line diff
--- a/emboss_iep.xml	Thu Feb 23 09:43:32 2017 -0500
+++ b/emboss_iep.xml	Mon Apr 23 13:04:47 2018 -0400
@@ -15,7 +15,7 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out_file1" format="iep" />
+    <data name="out_file1" format="txt" />
   </outputs>
   <tests>
     <test>
--- a/emboss_tranalign.xml	Thu Feb 23 09:43:32 2017 -0500
+++ b/emboss_tranalign.xml	Mon Apr 23 13:04:47 2018 -0400
@@ -1,82 +1,90 @@
 <tool id="EMBOSS: tranalign100" name="tranalign" version="5.0.0">
-  <description>Align nucleic coding regions given the aligned proteins</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-  <code file="emboss_format_corrector.py" />
-  <command>tranalign -asequence '$input1' -bsequence '$input2' -outseq '$out_file1' -table $table -osformat3 $out_format1 -auto</command>
-  <inputs>
-    <param name="input1" type="data" format="fasta" label="Nucleic sequences" />
-    <param name="input2" type="data" format="data" label="Protein sequences" />
-    <param name="table" type="select" label="Code to use">
-      <option value="0">Standard</option>
-      <option value="1">Standard (with alternative initiation codons)</option>
-      <option value="2">Vertebrate Mitochondrial</option>
-      <option value="3">Yeast Mitochondrial</option>
-      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
-      <option value="5">Invertebrate Mitochondrial</option>
-      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
-      <option value="9">Echinoderm Mitochondrial</option>
-      <option value="10">Euplotid Nuclear</option>
-      <option value="11">Bacterial</option>
-      <option value="12">Alternative Yeast Nuclear</option>
-      <option value="13">Ascidian Mitochondrial</option>
-      <option value="14">Flatworm Mitochondrial</option>
-      <option value="15">Blepharisma Macronuclear</option>
-      <option value="16">Chlorophycean Mitochondrial</option>
-      <option value="21">Trematode Mitochondrial</option>
-      <option value="22">Scenedesmus obliquus</option>
-      <option value="23">Thraustochytrium Mitochondrial</option>
-    </param>
-    <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>
-      <param name="input1" value="3.fasta"/>
-      <param name="input2" value="2.pep"/>
-      <param name="table" value="0"/>
-      <param name="out_format1" value="fasta"/>
-      <output name="out_file1" file="emboss_tranalign_out.fasta"/>
-    </test>
-  </tests>
-  <help>
-    You can view the original documentation here_.
+    <description>Align nucleic coding regions given the aligned proteins</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="emboss_format_corrector.py" />
+    <command detect_errors="aggressive"><![CDATA[
+tranalign
+-asequence '$input1'
+-bsequence '$input2'
+-outseq '$out_file1'
+-table $table
+-osformat3 $out_format1
+-auto
+    ]]></command>
+    <inputs>
+        <param name="input1" argument="-asequence" type="data" format="fasta" label="Nucleic sequences" />
+        <param name="input2" argument="-bsequence" type="data" format="data" label="Protein sequences" />
+        <param argument="-table" type="select" label="Code to use">
+            <option value="0">Standard</option>
+            <option value="1">Standard (with alternative initiation codons)</option>
+            <option value="2">Vertebrate Mitochondrial</option>
+            <option value="3">Yeast Mitochondrial</option>
+            <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+            <option value="5">Invertebrate Mitochondrial</option>
+            <option value="6">Ciliate Macronuclear and Dasycladacean</option>
+            <option value="9">Echinoderm Mitochondrial</option>
+            <option value="10">Euplotid Nuclear</option>
+            <option value="11">Bacterial</option>
+            <option value="12">Alternative Yeast Nuclear</option>
+            <option value="13">Ascidian Mitochondrial</option>
+            <option value="14">Flatworm Mitochondrial</option>
+            <option value="15">Blepharisma Macronuclear</option>
+            <option value="16">Chlorophycean Mitochondrial</option>
+            <option value="21">Trematode Mitochondrial</option>
+            <option value="22">Scenedesmus obliquus</option>
+            <option value="23">Thraustochytrium Mitochondrial</option>
+        </param>
+        <param name="out_format1" argument="-osformat3" 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>
+            <param name="input1" value="3.fasta"/>
+            <param name="input2" value="2.pep"/>
+            <param name="table" value="0"/>
+            <param name="out_format1" value="fasta"/>
+            <output name="out_file1" file="emboss_tranalign_out.fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+You can view the original documentation here_.
 
-    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html
-  </help>
-  <expand macro="citations" />
+.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/tranalign.html
+    ]]></help>
+    <expand macro="citations" />
 </tool>
--- a/emboss_transeq.xml	Thu Feb 23 09:43:32 2017 -0500
+++ b/emboss_transeq.xml	Mon Apr 23 13:04:47 2018 -0400
@@ -1,130 +1,129 @@
 <tool id="EMBOSS: transeq101" name="transeq" version="5.0.0">
-  <description>Translate nucleic acid sequences</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements" />
-  <code file="emboss_format_corrector.py" />
-  <command><![CDATA[
-    transeq 
-      -sequence '$input1' 
-      -outseq '$out_file1' 
-      -frame $frame 
-      -table $table
-      #if str($regions).strip():
-        -regions '$regions'
-      #end if
-      -trim $trim 
-      -clean $clean 
-      -alternative $alternative 
-      -osformat2 '$out_format1' 
-      -auto
-  ]]>
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="fasta" label="Sequences" />
-    <param name="frame" type="select" label="Frame(s) to translate">
-      <option value="1">Frame 1</option>
-      <option value="2">Frame 2</option>
-      <option value="3">Frame 3</option>
-      <option value="F">Forward three frames</option>
-      <option value="-1">Frame -1</option>
-      <option value="-2">Frame -2</option>
-      <option value="-3">Frame -3</option>
-      <option value="R">Reverse three frames</option>
-      <option value="6">All six frames</option>
-    </param>
-    <param name="table" type="select" label="Code to use">
-      <option value="0">Standard</option>
-      <option value="1">Standard (with alternative initiation codons)</option>
-      <option value="2">Vertebrate Mitochondrial</option>
-      <option value="3">Yeast Mitochondrial</option>
-      <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
-      <option value="5">Invertebrate Mitochondrial</option>
-      <option value="6">Ciliate Macronuclear and Dasycladacean</option>
-      <option value="9">Echinoderm Mitochondrial</option>
-      <option value="10">Euplotid Nuclear</option>
-      <option value="11">Bacterial</option>
-      <option value="12">Alternative Yeast Nuclear</option>
-      <option value="13">Ascidian Mitochondrial</option>
-      <option value="14">Flatworm Mitochondrial</option>
-      <option value="15">Blepharisma Macronuclear</option>
-      <option value="16">Chlorophycean Mitochondrial</option>
-      <option value="21">Trematode Mitochondrial</option>
-      <option value="22">Scenedesmus obliquus</option>
-      <option value="23">Thraustochytrium Mitochondrial</option>
-    </param>
-    <param name="regions" type="text" value="" label="Regions to translate" />
-    <param name="trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <param name="alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
-      <option value="no">No</option>
-      <option value="yes">Yes</option>
-    </param>
-    <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>
-      <param name="input1" value="2.fasta"/>
-      <param name="frame" value="1"/>
-      <param name="table" value="0"/>
-      <param name="regions" value=""/>
-      <param name="trim" value="no"/>
-      <param name="clean" value="no"/>
-      <param name="alternative" value="no"/>
-      <param name="out_format1" value="fasta"/>
-      <output name="out_file1" file="emboss_transeq_out.fasta"/>
-    </test>
-  </tests>
-  <help>
+    <description>Translate nucleic acid sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <code file="emboss_format_corrector.py" />
+    <command detect_errors="aggressive"><![CDATA[
+transeq
+-sequence '$input1'
+-outseq '$out_file1'
+-frame $frame
+-table $table
+#if str($regions).strip():
+    -regions '$regions'
+#end if
+-trim $trim
+-clean $clean
+-alternative $alternative
+-osformat2 '$out_format1'
+-auto
+    ]]></command>
+    <inputs>
+        <param name="input1" argument="-sequence" type="data" format="fasta" label="Sequences" />
+        <param argument="-frame" type="select" label="Frame(s) to translate">
+            <option value="1">Frame 1</option>
+            <option value="2">Frame 2</option>
+            <option value="3">Frame 3</option>
+            <option value="F">Forward three frames</option>
+            <option value="-1">Frame -1</option>
+            <option value="-2">Frame -2</option>
+            <option value="-3">Frame -3</option>
+            <option value="R">Reverse three frames</option>
+            <option value="6">All six frames</option>
+        </param>
+        <param argument="-table" type="select" label="Code to use">
+            <option value="0">Standard</option>
+            <option value="1">Standard (with alternative initiation codons)</option>
+            <option value="2">Vertebrate Mitochondrial</option>
+            <option value="3">Yeast Mitochondrial</option>
+            <option value="4">Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+            <option value="5">Invertebrate Mitochondrial</option>
+            <option value="6">Ciliate Macronuclear and Dasycladacean</option>
+            <option value="9">Echinoderm Mitochondrial</option>
+            <option value="10">Euplotid Nuclear</option>
+            <option value="11">Bacterial</option>
+            <option value="12">Alternative Yeast Nuclear</option>
+            <option value="13">Ascidian Mitochondrial</option>
+            <option value="14">Flatworm Mitochondrial</option>
+            <option value="15">Blepharisma Macronuclear</option>
+            <option value="16">Chlorophycean Mitochondrial</option>
+            <option value="21">Trematode Mitochondrial</option>
+            <option value="22">Scenedesmus obliquus</option>
+            <option value="23">Thraustochytrium Mitochondrial</option>
+        </param>
+        <param argument="-regions" type="text" value="" label="Regions to translate" />
+        <param argument="-trim" type="select" label="Remove all 'X' and '*' characters from the right end of the translation">
+            <option value="no">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param argument="-clean" type="select" label="Change all STOP codon positions from the '*' character to 'X'">
+            <option value="no">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param argument="-alternative" type="select" label="Define frame '-1' as using the set of codons starting with the last codon of the sequence">
+            <option value="no">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="out_format1" argument="-osformat2" 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>
+            <param name="input1" value="2.fasta"/>
+            <param name="frame" value="1"/>
+            <param name="table" value="0"/>
+            <param name="regions" value=""/>
+            <param name="trim" value="no"/>
+            <param name="clean" value="no"/>
+            <param name="alternative" value="no"/>
+            <param name="out_format1" value="fasta"/>
+            <output name="out_file1" file="emboss_transeq_out.fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
 .. class:: warningmark
 
 The input dataset needs to be sequences.
 
 -----
 
-    You can view the original documentation here_.
+You can view the original documentation here_.
 
-    .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
-  </help>
-  <expand macro="citations" />
+.. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/transeq.html
+    ]]></help>
+    <expand macro="citations" />
 </tool>
--- a/test-data/emboss_cai_out.cai	Thu Feb 23 09:43:32 2017 -0500
+++ b/test-data/emboss_cai_out.cai	Mon Apr 23 13:04:47 2018 -0400
@@ -1,1 +1,1 @@
-Sequence: Sequence CAI: 0.188
\ No newline at end of file
+Sequence: Sequence CAI: 0.188
--- a/test-data/emboss_newcpgseek_out.newcpgseek	Thu Feb 23 09:43:32 2017 -0500
+++ b/test-data/emboss_newcpgseek_out.newcpgseek	Mon Apr 23 13:04:47 2018 -0400
@@ -6,4 +6,4 @@
  Begin    End  Score        CpG  %CG  CG/GC
    121    141    34          3  57.1   1.00
    261    272    43          3  75.0   1.00
--------------------------------------------
\ No newline at end of file
+-------------------------------------------
--- a/test-data/emboss_tranalign_out.fasta	Thu Feb 23 09:43:32 2017 -0500
+++ b/test-data/emboss_tranalign_out.fasta	Mon Apr 23 13:04:47 2018 -0400
@@ -42,4 +42,4 @@
 ctgactaccctggaagtaggccgcatgctttttgga---ggtaaagttcatggttccctg
 gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
 aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
-cccacctttggcaagaagaagggccccaatgccaactct
\ No newline at end of file
+cccacctttggcaagaagaagggccccaatgccaactct