Mercurial > repos > iuc > qiime_alpha_rarefaction
diff alpha_rarefaction.xml @ 0:d493a0d5d5f5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:36:01 -0400 |
| parents | |
| children | 0a097fc6e5a6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alpha_rarefaction.xml Thu May 18 09:36:01 2017 -0400 @@ -0,0 +1,162 @@ +<tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0"> + <description>A workflow script for performing alpha rarefaction</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <version_command>alpha_rarefaction.py --version</version_command> + <command detect_errors="aggressive"><![CDATA[ + ## set matplotlib backend + echo "backend:agg" > matplotlibrc && + + alpha_rarefaction.py + --otu_table_fp '$otu_table_fp' + --mapping_fp '$mapping_fp' + -o alpha_rarefaction + #if $parameter_fp + --parameter_fp '$parameter_fp' + #end if + --num_steps '$num_steps' + $parallel + -O "\${GALAXY_SLOTS:-4}" + #if $tree_fp + --tree_fp '$tree_fp' + #end if + --min_rare_depth '$min_rare_depth' + #if $max_rare_depth + --max_rare_depth '$max_rare_depth' + #end if + $retain_intermediate_files + + && mkdir -p $alpha_rarefaction_plots.files_path + && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots + && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path + ]]></command> + <inputs> + <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/> + <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/> + <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/> + <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/> + <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/> + <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="True" label="Tree file (optional)" help="Required for phylogenetic measures"/> + <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/> + <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/> + <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/> + </inputs> + <outputs> + <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/> + <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information"> + <discover_datasets pattern="(?P<designation>.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/> + </collection> + <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables"> + <discover_datasets pattern="rarefaction_(?P<designation>.+)\.biom" directory="alpha_rarefaction/rarefaction/"/> + <filter>retain_intermediate_files!=''</filter> + </collection> + <collection name="alpha_div" type="list" label="${tool.name} on ${on_string}: Alpha diversity results"> + <discover_datasets pattern="alpha_rarefaction_(?P<designation>.+)\.txt" directory="alpha_rarefaction/alpha_div/"/> + <filter>retain_intermediate_files!=''</filter> + </collection> + </outputs> + <tests> + <test> + <param name="otu_table_fp" value="alpha_rarefaction/otu_table.biom"/> + <param name="mapping_fp" value="alpha_rarefaction/mapping_file.txt"/> + <param name="num_steps" value="2"/> + <param name="parallel" value=""/> + <param name="tree_fp" value="alpha_rarefaction/rep_set.tre"/> + <param name="min_rare_depth" value="10"/> + <param name="max_rare_depth" value="50"/> + <param name="retain_intermediate_files" value="--retain_intermediate_files"/> + <output name="alpha_rarefaction_plots"> + <assert_contents> + <has_text text="Control_mouse_I.D._354" /> + </assert_contents> + </output> + <output_collection name="alpha_diversity" type="list" count="3"> + <element name="chao1"> + <assert_contents> + <has_text text="alpha_rarefaction_10_0" /> + <has_text text="alpha_rarefaction_30_5" /> + <has_text text="alpha_rarefaction_50_9" /> + </assert_contents> + </element> + <element name="observed_otus"> + <assert_contents> + <has_text text="alpha_rarefaction_10_0" /> + <has_text text="alpha_rarefaction_30_5" /> + <has_text text="alpha_rarefaction_50_9" /> + </assert_contents> + </element> + <element name="PD_whole_tree"> + <assert_contents> + <has_text text="alpha_rarefaction_10_0" /> + <has_text text="alpha_rarefaction_30_5" /> + <has_text text="alpha_rarefaction_50_9" /> + </assert_contents> + </element> + </output_collection> + <output_collection name="rarefaction" type="list" count="30"> + <element name="10_0"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + <element name="30_6"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + <element name="50_9"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + </output_collection> + <output_collection name="alpha_div" type="list" count="30"> + <element name="10_0"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + <element name="30_6"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + <element name="50_9"> + <assert_contents> + <has_text text="PC.636" /> + <has_text text="PC.354" /> + <has_text text="PC.634" /> + </assert_contents> + </element> + </output_collection> + </test> + </tests> + <help><![CDATA[ +**What it does** + +This script performs alpha rarefaction in several steps: + + - Generation of rarefied OTU tables + - Computation of alpha diversity metrics for each rarefied OTU table + - Concatenation of alpha diversity results + - Generation of alpha rarefaction plots + +More information about this tool is available on +`QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_. + ]]></help> + <citations> + <expand macro="citations"/> + </citations> +</tool>