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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 03:54:47 -0400 |
parents | f9df45b8425a |
children | 205f4c9739c0 |
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<tool id="qiime_jackknifed_beta_diversity" name="Perform jackknifed UPGMA clustering" version="@WRAPPER_VERSION@.0"> <description>and building jackknifed PCoA plots</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <stdio> <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> <regex match="RuntimeWarning: The result contains negative eigenvalues" source="both" level="warning" description="Presence of negative eigenvalues"/> </stdio> <version_command>jackknifed_beta_diversity.py --version</version_command> <command detect_errors="aggressive"><![CDATA[ jackknifed_beta_diversity.py --otu_table_fp '$otu_table_fp' --mapping_fp '$mapping_fp' -o jackknifed_beta_diversity --seqs_per_sample '$seqs_per_sample' #if $tree_fp --tree_fp '$tree_fp' #end if #if $parameter_fp --parameter_fp '$parameter_fp' #end if --master_tree '$master_tree' $parallel -O "\${GALAXY_SLOTS:-4}" && python $__tool_directory__/jackknifed_beta_diversity_output_management.py --data_directory jackknifed_beta_diversity --html_file '$jackknifed_beta_diversity_report' --html_dir '$jackknifed_beta_diversity_report.files_path' ]]></command> <inputs> <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" label="OTU table" multiple="True"/> <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" multiple="True"/> <param argument="--seqs_per_sample" type="integer" value="" label="Number of sequences to include in each jackknifed subset"/> <param argument="--tree_fp" type="data" format="txt" label="Tree file" help="It is required for phylogenetic measures" optional="True"/> <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/> <param argument="--master_tree" type="select" label="Method for computing master trees in jackknife analysis"> <option value="consensus" selected="True">Consensus of trees from jackknifed otu tables</option> <option value="full">Tree generated from input (unsubsambled) otu table</option> </param> <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/> </inputs> <outputs> <collection name="unrarefied_beta_div_dist_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for unrarefied beta diversity"> <discover_datasets pattern="(?P<designation>.+)\.txt" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/> </collection> <collection name="unrarefied_beta_div_tree" type="list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity"> <discover_datasets pattern="(?P<designation>.+)\.tre" directory="jackknifed_beta_diversity/unrarefied_bdiv/"/> </collection> <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables"> <discover_datasets pattern="rarefaction_(?P<designation>.+)\.biom" directory="jackknifed_beta_diversity/rarefaction/"/> </collection> <collection name="pcoa" type="list:list" label="${tool.name} on ${on_string}: PCoA"> <discover_datasets pattern="pcoa_(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/pcoa/"/> </collection> <collection name="rare_dm" type="list:list" label="${tool.name} on ${on_string}: Distance matrix for rarefied beta diversity"> <discover_datasets pattern="(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.txt" ext="txt" directory="jackknifed_beta_diversity/rare_dm/"/> </collection> <collection name="rare_upgma" type="list:list" label="${tool.name} on ${on_string}: UPGMA trees for unrarefied beta diversity"> <discover_datasets pattern="upgma_(?P<identifier_0>.+)_rarefaction_(?P<identifier_1>.+)\.tre" ext="txt" directory="jackknifed_beta_diversity/rare_upgma/"/> </collection> <collection name="rare_upgma_consensus" type="list" label="${tool.name} on ${on_string}: Consensus UPGMA trees for unrarefied beta diversity"> <discover_datasets pattern="(?P<designation>.+)\.tre" directory="jackknifed_beta_diversity/rare_upgma_consensus/"/> </collection> <data name="jackknifed_beta_diversity_report" format="html" label="${tool.name} on ${on_string}: Report"/> </outputs> <tests> <test> <param name="otu_table_fp" value="jackknifed_beta_diversity/otu_table.biom"/> <param name="mapping_fp" value="jackknifed_beta_diversity/map.txt"/> <param name="seqs_per_sample" value="10"/> <param name="tree_fp" value="jackknifed_beta_diversity/rep_set.tre"/> <param name="master_tree" value="consensus"/> <param name="parallel" value="--parallel"/> <output_collection name="unrarefied_beta_div_dist_matrix" type="list" count="2"/> <output_collection name="unrarefied_beta_div_tree" type="list" count="2"/> <output_collection name="rarefaction" type="list" count="10"/> <output_collection name="pcoa" type="list:list"> <element name="unweighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> <element name="weighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> </output_collection> <output_collection name="rare_dm" type="list:list"> <element name="unweighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> <element name="weighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> </output_collection> <output_collection name="rare_upgma" type="list:list"> <element name="unweighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> <element name="weighted_unifrac"> <element name="10_0"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </element> </output_collection> <output_collection name="rare_upgma_consensus" type="list" count="2"> <element name="unweighted_unifrac"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> <element name="weighted_unifrac"> <assert_contents> <has_text text="PC.636" /> <has_text text="PC.635" /> <has_text text="PC.356" /> <has_text text="PC.481" /> <has_text text="PC.354" /> <has_text text="PC.593" /> <has_text text="PC.355" /> <has_text text="PC.607" /> <has_text text="PC.634" /> </assert_contents> </element> </output_collection> <output name="jackknifed_beta_diversity_report"> <assert_contents> <has_text text="unweighted_unifrac" /> <has_text text="weighted_unifrac" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **What it does** This tool performs jackknifing (repeatedly resampling a subset of the available data from each sample) to measure robustness of individual UPGMA clusters and clusters in PCoA plots. More information about this tool is available on `QIIME documentation <http://qiime.org/scripts/jackknifed_beta_diversity.html>`_. ]]></help> <citations> <expand macro="citations"/> </citations> </tool>