Mercurial > repos > iuc > qiime_jackknifed_beta_diversity
diff jackknifed_beta_diversity.xml @ 0:f9df45b8425a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:31:46 -0400 |
| parents | |
| children | 205f4c9739c0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/jackknifed_beta_diversity.xml Thu May 18 09:31:46 2017 -0400 @@ -0,0 +1,223 @@ +<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>