Mercurial > repos > iuc > qiime_assign_taxonomy

diff assign_taxonomy.xml @ 5:b4170e1a3b85 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:30:05 -0400
parents ec3c4654eacc
children 7cebb6ea8c23
line wrap: on
line diff
--- a/assign_taxonomy.xml	Mon Jul 10 16:41:19 2017 -0400
+++ b/assign_taxonomy.xml	Sat Aug 05 07:30:05 2017 -0400
@@ -1,5 +1,5 @@
 <tool id="qiime_assign_taxonomy" name="Assign taxonomy" version="@WRAPPER_VERSION@.0">
-    <description>to each sequence</description>
+    <description> to each sequence (assign_taxonomy)</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,63 +11,62 @@
     </expand>
     <version_command>assign_taxonomy.py --version</version_command>
     <command detect_errors="aggressive"><![CDATA[
-        assign_taxonomy.py
-            --input_fasta_fp '$input_fasta_fp'
-            #if $id_to_taxonomy_condition.source_selector == 'history'
-                --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp'
-            #else if $id_to_taxonomy_condition.source_selector == 'cached'
-                --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp.fields.path'
-            #end if
-            --assignment_method '$methodcond.assignment_method'
-            #if $methodcond.assignment_method == "uclust"
-                --min_consensus_fraction '$methodcond.min_consensus_fraction'
-                --similarity '$methodcond.similarity'
-                --uclust_max_accepts '$methodcond.uclust_max_accepts'
-            #else if $methodcond.assignment_method == "rdp"
-                #if $methodcond.references.source_selector == 'history'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
-                #else if $methodcond.references.source_selector == 'cached'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
-                #end if
-                --confidence '$methodcond.confidence'
-            #else if $methodcond.assignment_method == "blast"
-                #if $methodcond.references.source_selector == 'history'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
-                #else if $methodcond.references.source_selector == 'cached'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
-                #end if
-                --blast_e_value '$methodcond.blast_e_value'
-            #else if $methodcond.assignment_method == "rtax"
-                --read_1_seqs_fp '$methodcond.read_1_seqs_fp'
-                --read_2_seqs_fp '$methodcond.read_2_seqs_fp'
-                $methodcond.single_ok
-                $methodcond.no_single_ok_generic
-                --read_id_regex '$methodcond.read_id_regex'
-                --amplicon_id_regex '$methodcond.amplicon_id_regex'
-                --header_id_rege '$methodcond.header_id_regex'
-            #else if $methodcond.assignment_method == "mothur"
-                #if $methodcond.references.source_selector == 'history'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
-                #else if $methodcond.references.source_selector == 'cached'
-                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
-                #end if
-                --confidence '$methodcond.confidence'
-            #else if $methodcond.assignment_method == "sortmerna"
-                --sortmerna_threads \${GALAXY_SLOTS:-1}
-                #if $methodcond.sortmerna_db
-                    --sortmerna_db '$methodcond.sortmerna_db'
-                #end if
-                --min_consensus_fraction '$methodcond.min_consensus_fraction'
-                --similarity '$methodcond.similarity'
-                --sortmerna_e_value '$methodcond.sortmerna_e_value'
-                --sortmerna_coverage '$methodcond.sortmerna_coverage'
-                --sortmerna_best_N_alignments '$methodcond.sortmerna_best_N_alignments'
-            #end if
-            -o assign_taxonomy
+assign_taxonomy.py
+    --input_fasta_fp '$input_fasta_fp'
+    #if $id_to_taxonomy_condition.source_selector == 'history'
+        --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp'
+    #else if $id_to_taxonomy_condition.source_selector == 'cached'
+        --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp.fields.path'
+    #end if
+    --assignment_method '$methodcond.assignment_method'
+    #if $methodcond.assignment_method == "uclust"
+        --min_consensus_fraction '$methodcond.min_consensus_fraction'
+        --similarity '$methodcond.similarity'
+        --uclust_max_accepts '$methodcond.uclust_max_accepts'
+    #else if $methodcond.assignment_method == "rdp"
+        #if $methodcond.references.source_selector == 'history'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
+        #else if $methodcond.references.source_selector == 'cached'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
+        #end if
+        --confidence '$methodcond.confidence'
+    #else if $methodcond.assignment_method == "blast"
+        #if $methodcond.references.source_selector == 'history'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
+        #else if $methodcond.references.source_selector == 'cached'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
+        #end if
+        --blast_e_value '$methodcond.blast_e_value'
+    #else if $methodcond.assignment_method == "rtax"
+        --read_1_seqs_fp '$methodcond.read_1_seqs_fp'
+        --read_2_seqs_fp '$methodcond.read_2_seqs_fp'
+        $methodcond.single_ok
+        $methodcond.no_single_ok_generic
+        --read_id_regex '$methodcond.read_id_regex'
+        --amplicon_id_regex '$methodcond.amplicon_id_regex'
+        --header_id_rege '$methodcond.header_id_regex'
+    #else if $methodcond.assignment_method == "mothur"
+        #if $methodcond.references.source_selector == 'history'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
+        #else if $methodcond.references.source_selector == 'cached'
+            --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
+        #end if
+        --confidence '$methodcond.confidence'
+    #else if $methodcond.assignment_method == "sortmerna"
+        --sortmerna_threads \${GALAXY_SLOTS:-1}
+        #if $methodcond.sortmerna_db
+            --sortmerna_db '$methodcond.sortmerna_db'
+        #end if
+        --min_consensus_fraction '$methodcond.min_consensus_fraction'
+        --similarity '$methodcond.similarity'
+        --sortmerna_e_value '$methodcond.sortmerna_e_value'
+        --sortmerna_coverage '$methodcond.sortmerna_coverage'
+        --sortmerna_best_N_alignments '$methodcond.sortmerna_best_N_alignments'
+    #end if
+    -o assign_taxonomy
     ]]></command>
     <inputs>
         <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file" />
-
         <conditional name="id_to_taxonomy_condition">
             <param name="source_selector" type="select" label="Do you want to use a taxonomy reference ?">
                 <option value="cached">Yes (from the local cache)</option>
@@ -75,16 +74,15 @@
                 <option value="void" selected="true">No</option>
             </param>
             <when value="cached">
-                <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy" type="select" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep">
+                <param argument="--id_to_taxonomy_fp" type="select" label="Tab-delimited file mapping sequences to assigned taxonomy" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep">
                     <options from_data_table="qiime_taxonomy"/>
                 </param>
             </when>
             <when value="history">
-                <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy"  type="data" format="tabular" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep"/>
+                <param argument="--id_to_taxonomy_fp" type="data" format="tabular" label="Tab-delimited file mapping sequences to assigned taxonomy" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep"/>
             </when>
             <when value="void"/>
         </conditional>
-
         <conditional name="methodcond">
             <param argument="--assignment_method" label="Taxon assignment method" type="select">
                 <option selected="True" value="uclust">uclust</option>