--- a/metaphlan.xml	Mon Jul 29 07:14:21 2024 +0000
+++ b/metaphlan.xml	Sun Aug 11 20:35:53 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+<tool id="metaphlan" name="MetaPhlAn" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>to profile the composition of microbial communities</description>
     <macros>
         <import>macros.xml</import>
@@ -15,8 +15,7 @@
                     <option value="s">Species only</option>
                 </param>
                 <when value="a">
-                    <param name="split_levels" type='boolean' checked="false" truevalue='true' falsevalue='false' 
-                        label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
+                    <param name="split_levels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a report for each taxonomic level?" help="It will be in addition to the default output"/>
                 </when>
                 <when value="k"/>
                 <when value="p"/>
@@ -261,10 +260,10 @@
                             <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ file with microbiota reads"/>
                         </when>
                         <when value="multiple">
-                            <param name="in" type="data" format="@FILE_FORMATS@" multiple="true" label="Single-end Fasta/FastQ files with microbiota reads"/>
+                            <param name="in" type="data" format="@FILE_FORMATS@" label="Single-end Fasta/FastQ files with microbiota reads" multiple="true"/>
                         </when>
                         <when value="paired_collection">
-                            <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads"/>
+                            <param name="in" type="data_collection" format="@FILE_FORMATS@" label="Paired-end Fasta/FastQ file with microbiota reads" collection_type="paired"/>
                         </when>
                         <when value="paired">
                             <param name="in_f" type="data" format="@FILE_FORMATS@" label="Forward paired-end Fasta/FastQ file with microbiota reads"/>
@@ -286,8 +285,7 @@
                     <param name="in" type="data" format="sam" label="Externally BowTie2-mapped SAM file" help="BowTie2 needs to be used first to map microbiota reads"/>
                 </when>
                 <when value="bowtie2out">
-                    <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" 
-                        help="File needs to be generated with MetaPhlAn versions >3.0"/>
+                    <param name="in" type="data" format="tabular" label="Intermediary mapping file of the microbiota generated by a previous MetaPhlAn run" help="File needs to be generated with MetaPhlAn versions &gt;3.0"/>
                 </when>
             </conditional>
             <conditional name="db">
@@ -317,7 +315,7 @@
                     <option value="reads_map">reads_map: Mapping from reads to clades (only reads hitting a marker)</option>
                     <option value="clade_profiles">clade_profiles: Normalized marker counts for clades with at least a non-null marker</option>
                     <option value="clade_specific_strain_tracker">clade_specific_strain_tracker: List of markers present for a specific clade and all its subclades</option>
-                    <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when > 0.0 and normalized by microbiota size if number of reads is specified)</option>
+                    <option value="marker_ab_table">marker_ab_table: Normalized marker counts (only when &gt; 0.0 and normalized by microbiota size if number of reads is specified)</option>
                     <option value="marker_counts">marker_counts: Non-normalized marker counts (use with extreme caution)</option>
                     <option value="marker_pres_table">marker_pres_table: List of markers present in the sample (threshold at 1.0 if not differently specified with --pres_th</option>
                 </param>
@@ -330,24 +328,20 @@
                 <when value="reads_map"/>
                 <when value="clade_profiles"/>
                 <when value="clade_specific_strain_tracker">
-                    <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present" 
-                        help="Markers are also extracted for subclades" />
+                    <param argument="--clade" type="text" value="" label="Clade for which to extract list of markers present" help="Markers are also extracted for subclades"/>
                     <param argument="--min_ab" type="float" optional="true" label="The minimum percentage abundance for the clade"/>
                 </when>
                 <when value="marker_ab_table">
-                    <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" 
-                        help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
+                    <param argument="--nreads" type="integer" optional="true" label="Total number of reads in the original microbiota" help="It is used for normalizing the length-normalized counts with the microbiota size as well. No normalization applied if the value is not specified"/>
                 </when>
                 <when value="marker_counts"/>
                 <when value="marker_pres_table">
                     <param argument="--pres_th" type="integer" optional="true" label="Threshold for calling a marker present"/>
                 </when>
             </conditional>
-            <param argument="--min_cu_len" type="integer" value="2000" 
-                label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
-            <param argument="--min_alignment_len" type="integer" optional="true" 
-                label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
-            <param name="organism_profiling" type="select" multiple="true" optional="true" label="Organisms to profile">
+            <param argument="--min_cu_len" type="integer" value="2000" label="Minimum total nucleotide length for the markers in a clade for estimating the abundance without considering sub-clade abundances"/>
+            <param argument="--min_alignment_len" type="integer" optional="true" label="Sam records for aligned reads with the longest subalignment length smaller than this threshold will be discarded."/>
+            <param name="organism_profiling" type="select" optional="true" label="Organisms to profile" multiple="true">
                 <option value="add_viruses" selected="true">Profile viral organisms (add_viruses)</option>
                 <option value="ignore_eukaryotes">Ignore eukaryotic organisms (ignore_eukaryotes)</option>
                 <option value="ignore_bacteria">Ignore bacteria organisms (ignore_bacteria)</option>
@@ -365,9 +359,7 @@
             <param argument="--stat_q" type="float" value="0.2" label="Quantile value for the robust average"/>
             <param argument="--perc_nonzero" type="float" value="0.33" label="Percentage of markers with a non zero relative abundance for misidentify a species"/>
             <param argument="--ignore_markers" type="data" format="txt,tabular" optional="true" label="File containing a list of markers to ignore" help="One marker per line"/>
-            <param argument="--avoid_disqm" type='boolean' checked="true" truevalue='--avoid_disqm' falsevalue='' 
-                label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?"
-                help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
+            <param argument="--avoid_disqm" type="boolean" truevalue="--avoid_disqm" falsevalue="" checked="true" label="Deactivate the procedure of disambiguating the quasi-markers based on the marker abundance pattern found in the sample?" help="It is generally recommended to keep the disambiguation procedure in order to minimize false positives"/>
         </section>
         <conditional name="subsample">
             <param name="selector" type="select" label="Subsample" help="Subsampling only works for fastq input">
@@ -377,11 +369,11 @@
             </param>
             <when value="no"/>
             <when value="single">
-                <param argument="--subsampling" type="integer" value="" min="1" label="Sumbsample reads" help="Specify the number of reads to be considered"/>
+                <param argument="--subsampling" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of reads to be considered"/>
                 <expand macro="subsample_common"/>
             </when>
             <when value="paired">
-                <param argument="--subsampling_paired" type="integer" value="" min="1" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/>
+                <param argument="--subsampling_paired" type="integer" min="1" value="" label="Sumbsample reads" help="Specify the number of paired reads to be considered. For N there will be floor(N/2) reads selected from the forward and reverse reads each."/>
                 <expand macro="subsample_common"/>
             </when>
         </conditional>
@@ -398,29 +390,25 @@
         <section name="out" title="Outputs" expanded="true">
             <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
             <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
-            <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue='' 
-                label="Use a species as representative for species groups?"/>
-            <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue='' 
-                label="Old MetaPhlAn2 two columns output?"/>
-            <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue='' 
-                label="Report the profiling using the CAMI output format?"/>
-            <param argument="--unclassified_estimation" type='boolean' checked="false" truevalue='--unclassified_estimation' falsevalue='' 
-                label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
-            <param name="krona_output" type='boolean' checked="false" truevalue='true' falsevalue='false' label="Output for Krona?"/>
+            <param argument="--use_group_representative" type="boolean" truevalue="--use_group_representative" falsevalue="" checked="false" label="Use a species as representative for species groups?"/>
+            <param argument="--legacy-output" type="boolean" truevalue="--legacy-output" falsevalue="" checked="false" label="Old MetaPhlAn2 two columns output?"/>
+            <param argument="--CAMI_format_output" type="boolean" truevalue="--CAMI_format_output" falsevalue="" checked="false" label="Report the profiling using the CAMI output format?"/>
+            <param argument="--unclassified_estimation" type="boolean" truevalue="--unclassified_estimation" falsevalue="" checked="false" label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
+            <param name="krona_output" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output for Krona?"/>
         </section>
         <!-- enabling this in tests will allow metaphlan to download reference data (we do this only with the smallish TOY DB) -->
         <param name="test" type="hidden" value="false"/>
     </inputs>
     <outputs>
-        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances" />
+        <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Predicted taxon relative abundances"/>
         <data name="bowtie2out" format="tabular" label="${tool.name} on ${on_string}: Bowtie2 output">
             <filter>inputs['in']['selector'] == "raw"</filter>
         </data>
         <data name="sam_output_file" format="sam" label="${tool.name} on ${on_string}: SAM file">
             <filter>inputs['in']['selector'] == "raw"</filter>
         </data>
-        <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file" />
-        <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels" >
+        <data name="biom_output_file" format="biom1" label="${tool.name} on ${on_string}: BIOM file"/>
+        <collection name="levels" type="list" label="${tool.name} on ${on_string}: Predicted taxon relative abundances at each taxonomic levels">
             <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="split_levels/" format="tabular"/>
             <filter>analysis['analysis_type']['t'] in ['rel_ab', 'rel_ab_w_read_stats'] and analysis['analysis_type']['tax_lev']['tax_lev'] == "a" and analysis['analysis_type']['tax_lev']['split_levels']</filter>
         </collection>
@@ -654,7 +642,7 @@
                     <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
                 </assert_contents>
             </output>
-            <output_collection name="levels" type="list" >
+            <output_collection name="levels" type="list">
                 <element name="all" ftype="tabular">
                     <assert_contents>
                         <has_text text="Gammaproteobacteria"/>
@@ -896,7 +884,6 @@
                     </assert_contents>
                 </element>
             </output_collection>
-
             <assert_stderr>
                 <has_text text="Downloading" negate="true"/>
             </assert_stderr>
@@ -992,7 +979,6 @@
                     </assert_contents>
                 </element>
             </output_collection>
-
             <assert_stderr>
                 <has_text text="Downloading" negate="true"/>
             </assert_stderr>
@@ -1179,7 +1165,7 @@
                     <has_text text="k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata"/>
                 </assert_contents>
             </output>
-            <output_collection name="levels" type="list" >
+            <output_collection name="levels" type="list">
                 <element name="all" ftype="tabular">
                     <assert_contents>
                         <has_text text="Gammaproteobacteria"/>
@@ -1309,7 +1295,8 @@
                 <has_text text="--vsc_out"/>
             </assert_command>
             <assert_stderr>
-                <has_text text="Downloading"/> <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->
+                <has_text text="Downloading"/>
+                <!-- due to test=true and the absence of the TOY reference DB Metaphlan will download to ~10MB-->
                 <has_text text="No reads aligning to VSC markers"/>
             </assert_stderr>
         </test>