# HG changeset patch
# User greg
# Date 1486562641 18000
# Node ID b468a86f87d98999f1daae82b53919c8edc576f6
# Parent  521d09ac701a71c80ccdb515c7df6627efa287b3
Uploaded

diff -r 521d09ac701a -r b468a86f87d9 assembly_post_processor.xml
--- a/assembly_post_processor.xml	Tue Jan 31 13:55:22 2017 -0500
+++ b/assembly_post_processor.xml	Wed Feb 08 09:04:01 2017 -0500
@@ -1,7 +1,7 @@
 <tool id="plant_tribes_assembly_post_processor" name="Postprocess de novo assembly transcripts" version="0.3">
     <description>into putative coding sequences</description>
     <requirements>
-        <requirement type="package" version="0.3">plant_tribes_assembly_post_processor</requirement>
+        <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -13,22 +13,18 @@
     </stdio>
     <command>
         <![CDATA[
-            #import os
             AssemblyPostProcesser
-            --transcripts '$input'
+            --transcripts "$input"
             --prediction_method $prediction_method_cond.prediction_method
             #if str($prediction_method_cond.prediction_method) == 'estscan':
-                --score_matrices '$score_matrices'
+                --score_matrices "$score_matrices"
             #end if
             #if str($options_type.options_type_selector) == 'advanced':
                 #if str($options_type.target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
-                    #set scaffold_path = $options_type.target_gene_family_assembly_cond.scaffold.fields.path
-                    #set scaffold_dir = $os.path.split($scaffold_path)[0]
-                    #set scaffold = $os.path.split($scaffold_path)[1]
-                    --gene_family_search '$options_type.target_gene_family_assembly_cond.orthogroups'
-                    --scaffold_dir $scaffold_dir
-                    --scaffold $scaffold
-                    --method '$options_type.target_gene_family_assembly_cond.method'
+                    --gene_family_search "$options_type.target_gene_family_assembly_cond.orthogroups"
+                    --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
+                    --scaffold "$options_type.target_gene_family_assembly_cond.scaffold"
+                    --method "$options_type.target_gene_family_assembly_cond.method"
                 #end if
                 --gap_trimming $options_type.gap_trimming
                 #if str($options_type.strand_specific) == 'yes':
@@ -102,11 +98,12 @@
         <test>
             <param name="input" value="assembly.fasta" ftype="fasta" />
             <param name="prediction_method" value="transdecoder" />
+            <param name="options_type_selector" value="basic" />
             <output_collection name="transcripts" type="list">
-                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta"/>
-                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta"/>
-                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta"/>
-                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta"/>
+                <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep1" ftype="fasta" compare="contains"/>
+                <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
             </output_collection>
         </test>
         <test>
@@ -120,7 +117,7 @@
                 <element name="transcripts.cds" file="transcripts.cds" ftype="fasta" compare="contains"/>
                 <element name="transcripts.cleaned.cds" file="transcripts.cleaned.cds" ftype="fasta" compare="contains"/>
                 <element name="transcripts.cleaned.nr.cds" file="transcripts.cleaned.nr.cds" ftype="fasta" compare="contains"/>
-                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.nr.pep" ftype="fasta" compare="contains"/>
+                <element name="transcripts.cleaned.nr.pep" file="transcripts.cleaned.pep" ftype="fasta" compare="contains"/>
                 <element name="transcripts.cleaned.pep" file="transcripts.cleaned.pep2" ftype="fasta" compare="contains"/>
                 <element name="transcripts.pep" file="transcripts.pep" ftype="fasta" compare="contains"/>
             </output_collection>
@@ -153,16 +150,8 @@
                 author = {Eric Wafula},
                 title = {None},
                 year = {None},
-                url = {https://github.com/dePamphilis/PlantTribes}
+                eprint = {None},
+                url = {None}
             }</citation>
-            <citation type="bibtex">
-                @published{Proc Int Conf Intell Syst Mol Biol,
-                author = {Iseli C, Jongeneel CV, Bucher P.},
-                title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences.},
-                year = {1999},
-                url = {http://estscan.sourceforge.net/}
-            }</citation>
-            <citation type="doi">10.1038/nprot.2013.084</citation>
-            <citation type="doi">10.1109/tcbb.2013.68</citation>
     </citations>
 </tool>