Mercurial > repos > iuc > qiime_align_seqs

diff align_seqs.xml @ 5:c97f432af74f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 88c494b035a34b097247a29bfd3515875d94ce2b
author iuc
date Fri, 04 Aug 2017 18:17:39 -0400
parents 31be13116b46
children b7b9c1d8b4d9
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line diff
--- a/align_seqs.xml	Mon Jul 10 16:32:22 2017 -0400
+++ b/align_seqs.xml	Fri Aug 04 18:17:39 2017 -0400
@@ -1,5 +1,5 @@
 <tool id="qiime_align_seqs" name="Align sequences" version="@WRAPPER_VERSION@.0">
-    <description>using a variety of alignment methods</description>
+    <description> using a variety of alignment methods (align_seqs)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -12,23 +12,23 @@
     </expand>
     <version_command>align_seqs.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        align_seqs.py
-            --input_fasta_fp '$input_fasta_fp'
-            -o output
-            --alignment_method '$alignment.alignment_method'
-            #if $alignment.alignment_method == 'pynast'
-                --pairwise_alignment_method '$alignment.pairwise_alignment_method'
-                #if str($alignment.template_fp) != 'None':
-                    --template_fp '$alignment.template_fp'
-                #end if
-            #elif $alignment.alignment_method == 'infernal'
-                --template_fp '$alignment.template_fp'
-            #end if
+align_seqs.py
+    --input_fasta_fp '$input_fasta_fp'
+    -o output
+    --alignment_method '$alignment.alignment_method'
+    #if $alignment.alignment_method == 'pynast'
+        --pairwise_alignment_method '$alignment.pairwise_alignment_method'
+        #if str($alignment.template_fp) != 'None':
+            --template_fp '$alignment.template_fp'
+        #end if
+    #elif $alignment.alignment_method == 'infernal'
+        --template_fp '$alignment.template_fp'
+    #end if
 
-            #if $min_length:
-                --min_length '$min_length'
-            #end if
-            --min_percent_id '$min_percent_id'
+    #if $min_length:
+        --min_length '$min_length'
+    #end if
+    --min_percent_id '$min_percent_id'
     ]]></command>
     <inputs>
         <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file"/>