diff assembly_post_processor.xml @ 74:9da5dc4b99cc draft

Uploaded

--- a/assembly_post_processor.xml	Thu Aug 24 13:04:03 2017 -0400
+++ b/assembly_post_processor.xml	Thu Oct 05 13:54:37 2017 -0400
@@ -1,9 +1,11 @@
-<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.2">
+<tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="@WRAPPER_VERSION@.3.0">
     <description>post-processes de novo transcriptome assembly</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements_assembly_post_processor" />
+    <requirements>
+        <requirement type="package" version="1.0.3">plant_tribes_assembly_post_processor</requirement>
+    </requirements>
     <command detect_errors="exit_code"><![CDATA[
 python '$__tool_directory__/assembly_post_processor.py'
 --transcripts '$input'
@@ -15,8 +17,7 @@
     #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 '$target_gene_family_assembly_cond.orthogroups'
-        --output_pttgf '$output_pttgf'
-        --output_pttgf_dir '$output_pttgf.files_path'
+        --move_stats true
         --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
         --method '$target_gene_family_assembly_cond.method'
         --gap_trimming $target_gene_family_assembly_cond.gap_trimming
@@ -89,9 +90,14 @@
         </conditional>
     </inputs>
     <outputs>
-        <data name="output_pttgf" format="pttgf" label="Targeted gene families: ${tool.name} on ${on_string}">
+        <collection name="output_tgf" 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" />
             <filter>options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes'</filter>
-        </data>
+        </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 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}">