diff humann2.xml @ 1:1d6d855c10d8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee

--- a/humann2.xml	Mon Mar 13 12:39:25 2017 -0400
+++ b/humann2.xml	Tue Aug 01 07:58:21 2017 -0400
@@ -12,110 +12,110 @@
     </expand>
     <expand macro="version"/>
     <command detect_errors="exit_code"><![CDATA[
-        #if $nucleotide_db.nucleotide_db_selector == "history"
-            mkdir nucleotide_db
-            &&
-            #for $file in $nucleotide_db.nucleotide_database:
-                cp '$file' 'nucleotide_db/$file.name' &&
-            #end for
-        #end if
+#if $nucleotide_db.nucleotide_db_selector == "history"
+    mkdir nucleotide_db
+    &&
+    #for $file in $nucleotide_db.nucleotide_database:
+        cp '$file' 'nucleotide_db/$file.name' &&
+    #end for
+#end if
 
-        #if $protein_db.protein_db_selector == "history"
-            mkdir protein_db
-            &&
-            #if $translated_alignment == "diamond"
-                diamond makedb
-                    --in '$protein_db.protein_database'
-                    --db 'protein_db/protein_db'
-                    --threads "\${GALAXY_SLOTS:-4}"
-            #else
-                prerapsearch 
-                    -d '$protein_db.protein_database'
-                    -n 'protein_db/protein_db'
-            #end if
-            &&
-        #end if
+#if $protein_db.protein_db_selector == "history"
+    mkdir protein_db
+    &&
+    #if $translated_alignment == "diamond"
+        diamond makedb
+            --in '$protein_db.protein_database'
+            --db 'protein_db/protein_db'
+            --threads "\${GALAXY_SLOTS:-4}"
+    #else
+        prerapsearch 
+            -d '$protein_db.protein_database'
+            -n 'protein_db/protein_db'
+    #end if
+    &&
+#end if
 
-        #if $taxo_profile.taxonomic_profile_test == "false"
-            #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
-                mkdir ref_db
-                &&
-                bowtie2-build '$taxo_profile.metaphlan2_db_choice.bowtie2db' 'ref_db/ref_db'
-                &&
-                python '$__tool_directory__/transform_json_to_pkl.py'
-                    --json_input '$taxo_profile.metaphlan2_db_choice.mpa_pkl'
-                    --pkl_output 'ref_db/metadata.pkl'
-                &&
-            #end if
-        #end if
+#if $taxo_profile.taxonomic_profile_test == "false"
+    #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
+        mkdir ref_db
+        &&
+        bowtie2-build '$taxo_profile.metaphlan2_db_choice.bowtie2db' 'ref_db/ref_db'
+        &&
+        python '$__tool_directory__/transform_json_to_pkl.py'
+            --json_input '$taxo_profile.metaphlan2_db_choice.mpa_pkl'
+            --pkl_output 'ref_db/metadata.pkl'
+        &&
+    #end if
+#end if
 
-        humann2
-            --input '$input'
-            -o 'output'
-            $bypass.bypass_prescreen
-            $bypass.bypass_nucleotide_index
-            $bypass.bypass_translated_search
-            $bypass.bypass_nucleotide_search
-            
-            #set $metaphlan_option = "-t rel_ab"
-            #if $taxo_profile.taxonomic_profile_test == "true":
-                --taxonomic-profile '$taxo_profile.taxonomic_profile'
-            #else
-                #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
-                    #set $metaphlan_option += " --bowtie2db " + 'ref_db/ref_db'
-                    #set $metaphlan_option += " --mpa_pkl " + 'ref_db/metadata.pkl'
-                #else
-                    #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
-                    #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
-                    #set $metaphlan_option += " --bowtie2db " + $path + "/" + $value
-                    #set $metaphlan_option += " --mpa_pkl " + $path + "/" + $value + ".pkl"
-                #end if
-            #end if
-            --metaphlan-options="$metaphlan_option"
+humann2
+    --input '$input'
+    -o 'output'
+    $bypass.bypass_prescreen
+    $bypass.bypass_nucleotide_index
+    $bypass.bypass_translated_search
+    $bypass.bypass_nucleotide_search
+    
+    #set $metaphlan_option = "-t rel_ab"
+    #if $taxo_profile.taxonomic_profile_test == "true":
+        --taxonomic-profile '$taxo_profile.taxonomic_profile'
+    #else
+        #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
+            #set $metaphlan_option += " --bowtie2db " + 'ref_db/ref_db'
+            #set $metaphlan_option += " --mpa_pkl " + 'ref_db/metadata.pkl'
+        #else
+            #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
+            #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
+            #set $metaphlan_option += " --bowtie2db " + $path + "/" + $value
+            #set $metaphlan_option += " --mpa_pkl " + $path + "/" + $value + ".pkl"
+        #end if
+    #end if
+    --metaphlan-options="$metaphlan_option"
 
-            #if $nucleotide_db.nucleotide_db_selector == "cached"
-                --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
-            #else
-                --nucleotide-database nucleotide_db
-            #end if
+    #if $nucleotide_db.nucleotide_db_selector == "cached"
+        --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
+    #else
+        --nucleotide-database nucleotide_db
+    #end if
 
-            --translated-alignment '$translated_alignment'
-            #if $protein_db.protein_db_selector == "cached"
-                --protein-database '$protein_db.protein_database.fields.path'
-            #else
-                --protein-database protein_db
-            #end if
-            --search-mode '$search_mode'
-            --pathways '$pathways' 
+    --translated-alignment '$translated_alignment'
+    #if $protein_db.protein_db_selector == "cached"
+        --protein-database '$protein_db.protein_database.fields.path'
+    #else
+        --protein-database protein_db
+    #end if
+    --search-mode '$search_mode'
+    --pathways '$pathways' 
 
-            --annotation-gene-index $adv.annotation_gene_index
-            --evalue '$adv.evalue'
-            --threads "\${GALAXY_SLOTS:-4}"
-            --memory-use minimum
-	        --prescreen-threshold '$adv.prescreen_threshold'
-            --identity-threshold '$adv.identity_threshold'
-            --translated-subject-coverage-threshold '$adv.translated_subject_coverage_threshold'
-            --translated-query-coverage-threshold '$adv.translated_query_coverage_threshold'
-            #if $adv.id_mapping
-                --id-mapping '$adv.id_mapping'
-            #end if
-            --xipe '$adv.xipe'
-            --minpath '$adv.minpath'
-            --pick-frames '$adv.pick_frames'
-            --gap-fill '$adv.gap_fill'
-            --output-format '$adv.output_format'
-            --output-max-decimals '$adv.output_max_dec'
-            --output-basename 'humann2'
-            $adv.remove_statified_output
-            $adv.remove_column_description_output
+    --annotation-gene-index $adv.annotation_gene_index
+    --evalue '$adv.evalue'
+    --threads "\${GALAXY_SLOTS:-4}"
+    --memory-use minimum
+    --prescreen-threshold '$adv.prescreen_threshold'
+    --identity-threshold '$adv.identity_threshold'
+    --translated-subject-coverage-threshold '$adv.translated_subject_coverage_threshold'
+    --translated-query-coverage-threshold '$adv.translated_query_coverage_threshold'
+    #if $adv.id_mapping
+        --id-mapping '$adv.id_mapping'
+    #end if
+    --xipe '$adv.xipe'
+    --minpath '$adv.minpath'
+    --pick-frames '$adv.pick_frames'
+    --gap-fill '$adv.gap_fill'
+    --output-format '$adv.output_format'
+    --output-max-decimals '$adv.output_max_dec'
+    --output-basename 'humann2'
+    $adv.remove_statified_output
+    $adv.remove_column_description_output
     ]]></command>
     <inputs>
         <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
         <section name="bypass" title="Options to bypass some steps" expanded="False">
-            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" checked="false" truevalue="--bypass-prescreen" falsevalue="" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
-            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" checked="false" truevalue="--bypass-nucleotide-index" falsevalue="" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
-            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" checked="false" truevalue="--bypass-translated-search" falsevalue="" label="Bypass the translated search step?"/>
-            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" checked="false" truevalue="--bypass-translated-search" falsevalue="" label="Bypass the nucleotide search steps?"/>
+            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
+            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
+            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
+            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>
         </section>
         <conditional name="taxo_profile">
             <param name="taxonomic_profile_test" type="select" label="Use a custom taxonomic profile?" help="The file must have been created by MetaPhlan2">
@@ -191,18 +191,18 @@
             <param name="identity_threshold" argument="--identity-threshold" type="float" value="50" label="Identity threshold for alignments"/>
             <param name="translated_subject_coverage_threshold" argument="--translated-subject-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
             <param name="translated_query_coverage_threshold" argument="--translated-query-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
-            <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" label="id mapping file for alignments" optional="True"/>
-            <param argument="--xipe" type="boolean" checked="false" truevalue="on" falsevalue="off" label="Use xipe computation?"/>
-            <param argument="--minpath" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use minpath computation?"/>
-            <param name="pick_frames" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use pick frames computation?" argument="--pick-frames"/>
-            <param name="gap_fill" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use gap fill computation?" argument="--gap-fill"/>
-            <param name="output_format" type="select" label="Format of the output files" argument="--output-format">
+            <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" optional="true" label="id mapping file for alignments"/>
+            <param argument="--xipe" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use xipe computation?"/>
+            <param argument="--minpath" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use minpath computation?"/>
+            <param name="pick_frames" argument="--pick-frames" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use pick frames computation?"/>
+            <param name="gap_fill" argument="--gap-fill" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use gap fill computation?"/>
+            <param name="output_format" argument="--output-format" type="select" label="Format of the output files">
                 <option value="tsv" selected="true">TSV</option>
                 <option value="biom">BIOM</option>
             </param>
-            <param name="output_max_dec" type="integer" value="10" label="Number of decimals to output" argument="--output-max-decimals"/>
-            <param name="remove_statified_output" type="boolean" checked="false" truevalue="--remove-stratified-output" falsevalue="" label="Remove stratification from output?" argument="--remove-stratified-output"/>
-            <param name="remove_column_description_output" type="boolean" checked="false" truevalue="--remove-column-description-output" falsevalue="" label="Remove stratification from output?" argument="--remove-column-description-output"/>
+            <param name="output_max_dec" argument="--output-max-decimals" type="integer" value="10" label="Number of decimals to output"/>
+            <param name="remove_statified_output" argument="--remove-stratified-output" type="boolean" truevalue="--remove-stratified-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
+            <param name="remove_column_description_output" argument="--remove-column-description-output" type="boolean" truevalue="--remove-column-description-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
             
         </section>
     </inputs>