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changeset 3:83b998fa34ea draft

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planemo upload commit f6412ce479ec7ea8984e82ea1b226a039133eea4
author iuc
date Thu, 10 Nov 2016 16:21:41 -0500
parents 2f9619adab91
children 20f1b45dea63
files kobas_annotate.xml kobas_identify.xml kobas_macros.xml repository_dependencies.xml
diffstat 4 files changed, 14 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/kobas_annotate.xml	Sat Nov 05 10:37:44 2016 -0400
+++ b/kobas_annotate.xml	Thu Nov 10 16:21:41 2016 -0500
@@ -3,9 +3,9 @@
     <macros>
         <import>kobas_macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
-    </requirements>
+
+    <expand macro="requirements"/>
+
     <stdio>
         <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
         <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
@@ -67,6 +67,7 @@
             -s '$species'
             -e '$evalue'
             -r $rank
+            -n "\${GALAXY_SLOTS:-4}"
             -c $coverage
             #if $ortholog.only == 'YES':
                 -z '$ortholog.species'
@@ -80,7 +81,7 @@
         ]]>
     </command>
     <inputs>
-        <param format="fasta" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
+        <param format="fasta,tabular,txt" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
         <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
             <option value="fasta:pro">FASTA protein sequence</option>
             <option value="fasta:nuc">FASTA nucleotide sequence</option>
--- a/kobas_identify.xml	Sat Nov 05 10:37:44 2016 -0400
+++ b/kobas_identify.xml	Thu Nov 10 16:21:41 2016 -0500
@@ -3,9 +3,8 @@
     <macros>
         <import>kobas_macros.xml</import>
     </macros>
-    <requirements>
-        <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
-    </requirements>
+
+    <expand macro="requirements"/>
 
     <command>
         <![CDATA[
--- a/kobas_macros.xml	Sat Nov 05 10:37:44 2016 -0400
+++ b/kobas_macros.xml	Thu Nov 10 16:21:41 2016 -0500
@@ -1,6 +1,11 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.3</token>
+    <token name="@WRAPPER_VERSION@">0.4</token>
     <token name="@KOBAS_VERSION@">2.1.1</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
+        </requirements>
+    </xml>
     <xml name="input_kobasdb">
         <param
             name="species"
--- a/repository_dependencies.xml	Sat Nov 05 10:37:44 2016 -0400
+++ b/repository_dependencies.xml	Thu Nov 10 16:21:41 2016 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the BLAST datatype definitions (e.g. the BLAST XML format).">
-    <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
+    <repository changeset_revision="01b38f20197e" name="blast_datatypes" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>