diff humann.xml @ 1:6b7622dda516 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 948cdafe28ae232b641a58bb7dc044d320feb294"

--- a/humann.xml	Wed May 12 09:06:30 2021 +0000
+++ b/humann.xml	Wed May 19 17:03:51 2021 +0000
@@ -150,7 +150,7 @@
             --search-mode '$wf.translated_search.protein_db.search_mode'
             #else
             --protein-database '$wf.translated_search.protein_db.protein_database.fields.path'
-                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.dbkey
+                #if 'uniref50' in $wf.translated_search.protein_db.protein_database.fields.value
             --search-mode 'uniref50'
                 #else
             --search-mode 'uniref90'
@@ -261,7 +261,9 @@
                 <option value="abundance">Pre-computed (typically gene) abundance tables</option>
             </param>
             <when value="raw">
-                <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Paired-end Fasta/FastQ files should be merged first"/>
+                <param name="input" type="data" format="fastq,fastq.gz,fasta,fasta.gz" 
+                label="Quality-controlled shotgun sequencing reads (metagenome (DNA reads) or metatranscriptome (RNA reads))" 
+                help="Paired-end Fasta/FastQ files should be merged first"/>
             </when>
             <when value="mapping">
                 <param name="input" type="data" format="sam,bam" label="Pre-computed mappings of reads to database sequences"/>
@@ -273,7 +275,7 @@
         <conditional name="wf">
             <param name="selector" type="select" label="Steps">
                 <option value="bypass_prescreen">Bypass the prescreen step and run on the full ChocoPhlAn database (--bypass-prescreen)</option>
-                <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species</option>
+                <option value="bypass_taxonomic_profiling">Bypass the taxonomic profiling step and creates a custom ChocoPhlAn database of the species provided afterwards</option>
                 <option value="bypass_nucleotide_index">Starts the workflow with the nucleotide alignment step using the provided indexed database (--bypass-nucleotide-index)</option>
                 <option value="bypass_nucleotide_search">Bypass all of the alignment steps before the translated search (--bypass_nucleotide-search)</option>
                 <option value="bypass_translated_search">Run all of the alignment steps except the translated search (--bypass_translated-search)</option>
@@ -284,7 +286,7 @@
                 <expand macro="translated_search"/>
             </when>
             <when value="bypass_taxonomic_profiling">
-                <param argument="--taxonomic-profile" type="data" format="tabular,txt" label="Taxonomic profile file"/>
+                <param argument="--taxonomic-profile" type="data" format="tabular,txt,tsv" label="Taxonomic profile file"/>
                 <expand macro="nucleotide_search"/>
                 <expand macro="translated_search"/>
             </when>
@@ -346,48 +348,48 @@
         </section>
     </inputs>
     <outputs>
-        <data format="tabular" name="gene_families_tsv" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
+        <data name="gene_families_tsv" format="tabular" from_work_dir="output/*_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >
             <filter>out['output_format'] == "tsv"</filter>
         </data>
-        <data format="biom1" name="gene_families_biom" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
+        <data name="gene_families_biom" format="biom1" from_work_dir="output/*_genefamilies.biom" label="${tool.name} on ${on_string}: Gene families and their abundance" >
             <filter>out['output_format'] == "biom"</filter>
         </data>
-        <data format="tabular" name="pathcoverage_tsv" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
+        <data name="pathcoverage_tsv" format="tabular" from_work_dir="output/*_pathcoverage.tsv" label="${tool.name} on ${on_string}: Pathways and their coverage" >
             <filter>out['output_format'] == "tsv"</filter>
         </data>
-        <data format="biom1" name="pathcoverage_biom" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
+        <data name="pathcoverage_biom" format="biom1" from_work_dir="output/*_pathcoverage.biom" label="${tool.name} on ${on_string}: Pathways and their coverage" >
             <filter>out['output_format'] == "biom"</filter>
         </data>
-        <data format="tabular" name="pathabundance_tsv" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
+        <data name="pathabundance_tsv" format="tabular" from_work_dir="output/*_pathabundance.tsv" label="${tool.name} on ${on_string}: Pathways and their abundance" >
             <filter>out['output_format'] == "tsv"</filter>
         </data>
-        <data format="biom1" name="pathabundance_biom" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" >
+        <data name="pathabundance_biom" format="biom1" from_work_dir="output/*_pathabundance.biom" label="${tool.name} on ${on_string}: Pathways and their abundance" >
             <filter>out['output_format'] == "biom"</filter>
         </data>
         <data format="txt" name="log" label="${tool.name} on ${on_string}: Log"/>
-        <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/*_humann_temp/*_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" >
-            <filter>"metaphlan_bowtie2" in out['intermediate_temp']</filter>
+        <data format="tabular" name="metaphlan_bowtie2" from_work_dir="output/*_temp/*_metaphlan_bowtie2.txt" label="${tool.name} on ${on_string}: MetaPhlAn Bowtie2 output" >
+            <filter>out['intermediate_temp'] and "metaphlan_bowtie2" in out['intermediate_temp']</filter>
         </data>
-        <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_humann_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" >
-            <filter>"metaphlan_bugs_list" in out['intermediate_temp']</filter>
+        <data format="tabular" name="metaphlan_bugs_list" from_work_dir="output/*_temp/*_metaphlan_bugs_list.tsv" label="${tool.name} on ${on_string}: MetaPhlAn bugs list" >
+            <filter>out['intermediate_temp'] and "metaphlan_bugs_list" in out['intermediate_temp']</filter>
         </data>
-        <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" >
-            <filter>"bowtie2_alignment" in out['intermediate_temp']</filter>
+        <data format="sam" name="bowtie2_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.sam" label="${tool.name} on ${on_string}: Bowtie2 alignment results" >
+            <filter>out['intermediate_temp'] and "bowtie2_alignment" in out['intermediate_temp']</filter>
         </data>
-        <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_humann_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >
-            <filter>"bowtie2_reduced_alignment" in out['intermediate_temp']</filter>
+        <data format="tabular" name="bowtie2_reduced_alignment" from_work_dir="output/*_temp/*_bowtie2_aligned.tsv" label="${tool.name} on ${on_string}: Bowtie2 reduced alignment results" >
+            <filter>out['intermediate_temp'] and "bowtie2_reduced_alignment" in out['intermediate_temp']</filter>
         </data>
-        <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_humann_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >
-            <filter>"bowtie2_unaligned" in out['intermediate_temp']</filter>
+        <data format="fasta" name="bowtie2_unaligned" from_work_dir="output/*_temp/*_bowtie2_unaligned.fa" label="${tool.name} on ${on_string}: Unaligned reads after Bowtie2" >
+            <filter>out['intermediate_temp'] and "bowtie2_unaligned" in out['intermediate_temp']</filter>
         </data>
-        <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_humann_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >
-            <filter>"custom_chocophlan_database" in out['intermediate_temp']</filter>
+        <data format="fasta" name="custom_chocophlan_database" from_work_dir="output/*_temp/*_custom_chocophlan_database.ffn" label="${tool.name} on ${on_string}: Custom ChocoPhlAn database" >
+            <filter>out['intermediate_temp'] and "custom_chocophlan_database" in out['intermediate_temp']</filter>
         </data>
-        <data format="tabular" name="diamond_aligned" from_work_dir="output/*_humann_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >
-            <filter>"diamond_aligned" in out['intermediate_temp']</filter>
+        <data format="tabular" name="diamond_aligned" from_work_dir="output/*_temp/*_diamond_aligned.tsv" label="${tool.name} on ${on_string}: Translated alignment results" >
+            <filter>out['intermediate_temp'] and "diamond_aligned" in out['intermediate_temp']</filter>
         </data>
-        <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_humann_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
-            <filter>"diamond_unaligned" in out['intermediate_temp']</filter>
+        <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
+            <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter>
         </data>
     </outputs>
     <tests>
@@ -591,7 +593,7 @@
             </section>
             <output name="gene_families_biom" ftype="biom1">
                 <assert_contents>
-                    <has_text text="http://biom-format.org"/>
+                    <has_text text="biom-format"/>
                     <has_text text="UniRef90_A0A396BPQ7|g__Bacteroides.s__Bacteroides_vulgatus"/>
                     <has_text text="UniRef90_W8YTG4|unclassified"/>
                 </assert_contents>
@@ -600,7 +602,7 @@
                 <assert_contents>
                     <has_text text="TREE"/>
                     <has_text text="format-url"/>
-                    <has_text text="http://biom-format.org"/>
+                    <has_text text="biom-format"/>
                     <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                     <has_text text="humann_Coverage"/>
                 </assert_contents>
@@ -609,7 +611,7 @@
                 <assert_contents>
                     <has_text text="TREE"/>
                     <has_text text="format-url"/>
-                    <has_text text="http://biom-format.org"/>
+                    <has_text text="biom-format"/>
                     <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified"/>
                     <has_text text="humann_Abundance"/>
                 </assert_contents>