Mercurial > repos > iuc > qiime_pick_closed_reference_otus
diff pick_closed_reference_otus.xml @ 0:2b6d3067087a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 04:02:18 -0400 |
parents | |
children | 935abbf93f99 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pick_closed_reference_otus.xml Fri May 19 04:02:18 2017 -0400 @@ -0,0 +1,153 @@ +<tool id="qiime_pick_closed_reference_otus" name="Perform closed-reference OTU picking" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>pick_closed_reference_otus.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + pick_closed_reference_otus.py + --input_fp '$input_fp' + --output_dir otus + #if str( $ref_seq.selector ) == 'history' + #set $ref = $ref_seq.reference_fp + #else + #set $ref = $ref_seq.reference_fp.fields.path + #end if + --reference_fp '$ref' + #if str( $taxonomy.selector ) == 'taxonomy_map' + #if str( $taxonomy.taxo_map.selector ) == 'history' + #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp + #else + #set $taxonomy = $taxonomy.taxo_map.taxonomy_fp.fields.path + #end if + --taxonomy_fp '$taxonomy' + #else if str( $taxonomy.selector ) == 'assign_taxonomy' + --assign_taxonomy + #else if str( $taxonomy.selector ) == 'suppress_taxonomy_assignment' + --suppress_taxonomy_assignment + #end if + #if $parameter_fp + --parameter_fp '$parameter_fp' + #end if + $parallel + -O "\${GALAXY_SLOTS:-4}" + ]]></command> + <inputs> + <param argument="--input_fp" type="data" format="fasta" label="Input sequence file"/> + <conditional name="ref_seq"> + <param name="selector" type="select" label="Reference sequences to query"> + <option value="cached" selected="True">Public databases</option> + <option value="history">Databases from your history</option> + </param> + <when value="cached"> + <param argument="--reference_fp" label="Reference sequences" type="select"> + <options from_data_table="qiime_rep_set"/> + </param> + </when> + <when value="history"> + <param argument="--reference_fp" type="data" format="fasta" label="Reference databases"/> + </when> + </conditional> + <conditional name="taxonomy"> + <param name="selector" type="select" label="Assign taxonomy?"> + <option value="taxonomy_map" selected="True">Assign taxonomy using a taxonomy map</option> + <option value="assign_taxonomy">Assign taxonomy to each sequence using assign_taxonomy.py</option> + <option value="suppress_taxonomy_assignment">Skip the taxonomy assignment step</option> + </param> + <when value="taxonomy_map"> + <conditional name="taxo_map"> + <param name="selector" type="select" label="Taxonomy map to use"> + <option value="cached" selected="True">Public taxonomy map</option> + <option value="history">Taxonomy map from your history</option> + </param> + <when value="cached"> + <param argument="--taxonomy_fp" label="Taxonomy map" type="select"> + <options from_data_table="qiime_taxonomy"/> + </param> + </when> + <when value="history"> + <param argument="--taxonomy_fp" type="data" format="txt" label="Taxonomy map"/> + </when> + </conditional> + </when> + <when value="assign_taxonomy"/> + <when value="suppress_taxonomy_assignment"/> + </conditional> + <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/> + <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/> + </inputs> + <outputs> + <data name="otu_table" format="biom1" from_work_dir="otus/otu_table.biom" label="${tool.name} on ${on_string}: OTU table"/> + </outputs> + <tests> + <test> + <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> + <conditional name="ref_seq"> + <param name="selector" value="history"/> + <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> + </conditional> + <conditional name="taxonomy"> + <param name="selector" value="taxonomy_map"/> + <conditional name="taxo_map"> + <param name="selector" value="history"/> + <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/> + </conditional> + </conditional> + <param name="parallel" value=""/> + <output name="otu_table" file="pick_closed_reference_otus/basic_otu_table.biom" compare="sim_size" /> + </test> + <test> + <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> + <conditional name="ref_seq"> + <param name="selector" value="history"/> + <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> + </conditional> + <conditional name="taxonomy"> + <param name="selector" value="taxonomy_map"/> + <conditional name="taxo_map"> + <param name="selector" value="history"/> + <param name="taxonomy_fp" value="pick_closed_reference_otus/taxa.txt"/> + </conditional> + </conditional> + <param name="parameter_fp" value="pick_closed_reference_otus/sortmerna_params.txt"/> + <param name="parallel" value=""/> + <output name="otu_table" file="pick_closed_reference_otus/sortmerna_otu_table.biom" compare="sim_size" /> + </test> + <test> + <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> + <conditional name="ref_seq"> + <param name="selector" value="history"/> + <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> + </conditional> + <conditional name="taxonomy"> + <param name="selector" value="assign_taxonomy"/> + </conditional> + <param name="parallel" value=""/> + <output name="otu_table" file="pick_closed_reference_otus/assign_taxonomy_otu_table.biom" compare="sim_size" /> + </test> + <test> + <param name="input_fps" value="pick_closed_reference_otus/seqs.fna"/> + <conditional name="ref_seq"> + <param name="selector" value="history"/> + <param name="reference_fp" value="pick_closed_reference_otus/refseqs.fna"/> + </conditional> + <conditional name="taxonomy"> + <param name="selector" value="suppress_taxonomy_assignment"/> + </conditional> + <param name="parallel" value=""/> + <output name="otu_table" file="pick_closed_reference_otus/suppress_taxonomy_assignment_otu_table.biom" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This script picks OTUs using a closed reference and constructs an OTU table. Taxonomy is assigned using a pre-defined taxonomy map of reference sequence OTU to taxonomy. If full-length genomes are provided as the reference sequences, this script applies the Shotgun UniFrac method. + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/pick_closed_reference_otus.html>`_. +]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>