diff assembly_post_processor.xml @ 70:cf4bf94e87d2 draft

Uploaded

--- a/assembly_post_processor.xml	Tue Jun 06 08:31:58 2017 -0400
+++ b/assembly_post_processor.xml	Wed Jun 07 10:01:51 2017 -0400
@@ -4,41 +4,39 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements_assembly_post_processor" />
-    <command detect_errors="exit_code">
-        <![CDATA[
-            python $__tool_directory__/assembly_post_processor.py
-            --transcripts '$input'
-            --prediction_method $prediction_method_cond.prediction_method
-            #if str($prediction_method_cond.prediction_method) == 'estscan':
-                --score_matrices '$score_matrices'
-            #end if
-            #if str($options_type.options_type_selector) == 'advanced':
-                #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 $output_pttgf.files_path
-                    --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
-                    --method '$target_gene_family_assembly_cond.method'
-                    --gap_trimming $target_gene_family_assembly_cond.gap_trimming
-                #end if
-                #if str($options_type.strand_specific) == 'yes':
-                    --strand_specific 'true'
-                #end if
-                #if str($options_type.dereplicate) == 'yes':
-                    --dereplicate 'true'
-                    --output_cleaned_nr_cds '$output_cleaned_nr_cds'
-                    --output_cleaned_nr_pep '$output_cleaned_nr_pep'
-                #end if
-                --min_length $options_type.min_length
-            #end if
-            --num_threads \${GALAXY_SLOTS:-4}
-            --output_cds '$output_cds'
-            --output_cleaned_cds '$output_cleaned_cds'
-            --output_cleaned_pep '$output_cleaned_pep'
-            --output_pep '$output_pep'
-        ]]>
-    </command>
+    <command detect_errors="exit_code"><![CDATA[
+python $__tool_directory__/assembly_post_processor.py
+--transcripts '$input'
+--prediction_method $prediction_method_cond.prediction_method
+#if str($prediction_method_cond.prediction_method) == 'estscan':
+    --score_matrices '$score_matrices'
+#end if
+#if str($options_type.options_type_selector) == 'advanced':
+    #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 $output_pttgf.files_path
+        --scaffold '$target_gene_family_assembly_cond.scaffold.fields.path'
+        --method '$target_gene_family_assembly_cond.method'
+        --gap_trimming $target_gene_family_assembly_cond.gap_trimming
+    #end if
+    #if str($options_type.strand_specific) == 'yes':
+        --strand_specific 'true'
+    #end if
+    #if str($options_type.dereplicate) == 'yes':
+        --dereplicate 'true'
+        --output_cleaned_nr_cds '$output_cleaned_nr_cds'
+        --output_cleaned_nr_pep '$output_cleaned_nr_pep'
+    #end if
+    --min_length $options_type.min_length
+#end if
+--num_threads \${GALAXY_SLOTS:-4}
+--output_cds '$output_cds'
+--output_cleaned_cds '$output_cleaned_cds'
+--output_cleaned_pep '$output_cleaned_pep'
+--output_pep '$output_pep'
+    ]]></command>
     <inputs>
         <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/>
         <conditional name="prediction_method_cond">