Mercurial > repos > greg > assembly_post_processor

changeset 78:cfb4b150fb3c draft

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Uploaded
author greg
date Thu, 05 Oct 2017 14:11:04 -0400
parents 2849bcb0b7ed
children 03716365973d
files assembly_post_processor.xml
diffstat 1 files changed, 4 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/assembly_post_processor.xml	Thu Oct 05 14:10:50 2017 -0400
+++ b/assembly_post_processor.xml	Thu Oct 05 14:11:04 2017 -0400
@@ -17,7 +17,8 @@
     #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond
     #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes':
         --gene_family_search '$target_gene_family_assembly_cond.orthogroups'
-        --move_stats true
+        --output_pttgf '$output_pttgf'
+        --output_pttgf_dir '$output_pttgf.files_path'
         --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
         --method '$target_gene_family_assembly_cond.method'
         --gap_trimming $target_gene_family_assembly_cond.gap_trimming
@@ -90,14 +91,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <collection name="output_stats" type="list" label="Targeted gene families statistics: ${tool.name} on ${on_string}">
-            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families_statistics" format="tabular" />
+        <data name="output_pttgf" format="pttgf" label="Targeted gene families: ${tool.name} on ${on_string}">
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
-        </collection>
-        <collection name="output_tgf" type="list" label="Targeted gene families: ${tool.name} on ${on_string}">
-            <discover_datasets pattern="__name__" directory="assemblyPostProcessing_dir/targeted_gene_families" format="fasta" />
-            <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
-        </collection>
+        </data>
         <data name="output_pep" format="fasta" label="transcripts.pep: ${tool.name} on ${on_string}"/>
         <data name="output_cleaned_pep" format="fasta" label="transcripts.cleaned.pep: ${tool.name} on ${on_string}"/>
         <data name="output_cleaned_nr_pep" format="fasta" label="transcripts.cleaned.nr.pep: ${tool.name} on ${on_string}">