Mercurial > repos > iuc > pick_closed_reference_otus

diff pick_closed_reference_otus.xml @ 0:768fb40ad1e8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
author iuc
date Thu, 18 May 2017 09:37:50 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pick_closed_reference_otus.xml	Thu May 18 09:37:50 2017 -0400
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+<tool id="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>