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comparison core_diversity_analyses.xml @ 5:486570c88d1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:14:36 -0400
parents 61e86fd975a4
children 57deb17cadbf
comparison
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4:52d3f0b8a78b 5:486570c88d1b
1 <tool id="qiime_core_diversity" name="Compute core set of diversity analyses" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_core_diversity" name="Run a core set of QIIME diversity analyses" version="@WRAPPER_VERSION@.0">
2 <description>A workflow for running a core set of QIIME diversity analyses</description> 2 <description>(core_diversity_analyses)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>core_diversity_analyses.py --version</version_command> 7 <version_command>core_diversity_analyses.py --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 ## set matplotlib backend 9 ## set matplotlib backend
10 echo "backend:agg" > matplotlibrc && 10 echo "backend:agg" > matplotlibrc &&
11 11
12 core_diversity_analyses.py 12 core_diversity_analyses.py
13 --input_biom_fp '$input_biom_fp' 13 --input_biom_fp '$input_biom_fp'
14 -o core_diversity_analyses 14 -o core_diversity_analyses
15 --mapping_fp '$mapping_fp' 15 --mapping_fp '$mapping_fp'
16 --sampling_depth '$sampling_depth' 16 --sampling_depth '$sampling_depth'
17 #if $parameter_fp 17 #if $parameter_fp
18 --parameter_fp '$parameter_fp' 18 --parameter_fp '$parameter_fp'
19 #end if 19 #end if
20 $parallel 20 $parallel
21 -O "\${GALAXY_SLOTS:-4}" 21 -O "\${GALAXY_SLOTS:-4}"
22 $phylogenetic.nonphylogenetic_diversity 22 $phylogenetic.nonphylogenetic_diversity
23 #if str( $phylogenetic.nonphylogenetic_diversity ) == "" 23 #if str( $phylogenetic.nonphylogenetic_diversity ) == ""
24 --tree_fp '$phylogenetic.tree_fp' 24 --tree_fp '$phylogenetic.tree_fp'
25 #end if 25 #end if
26 $suppress_taxa_summary 26 $suppress_taxa_summary
27 $suppress_beta_diversity 27 $suppress_beta_diversity
28 $suppress_alpha_diversity 28 $suppress_alpha_diversity
29 $suppress_group_significance 29 $suppress_group_significance
30 #if str( $categories ): 30 #if str( $categories ):
31 --categories '$categories' 31 --categories '$categories'
32 #end if 32 #end if
33 33
34 && mkdir -p '$html_report.files_path' 34 && mkdir -p '$html_report.files_path'
35 && cp -r core_diversity_analyses/* '$html_report.files_path' 35 && cp -r core_diversity_analyses/* '$html_report.files_path'
36 && mv '$html_report.files_path/index.html' '$html_report' 36 && mv '$html_report.files_path/index.html' '$html_report'
37 ]]></command> 37 ]]></command>
38 <inputs> 38 <inputs>
39 <param argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/> 39 <param argument="--input_biom_fp" type="data" format="tabular,txt,biom,h5" label="OTU table"/>
40 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" /> 40 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file" />
41 <param argument="--sampling_depth" type="integer" value="" label="Sequencing depth to use for even sub-sampling and maximum rarefaction depth" help="To decide this value, review the output of the ‘biom summarize-table’"/> 41 <param argument="--sampling_depth" type="integer" value="" label="Sequencing depth to use for even sub-sampling and maximum rarefaction depth" help="To decide this value, review the output of the ‘biom summarize-table’"/>
42 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/> 42 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file" help="It specifies changes to the default behavior" optional="true"/>
43 <param argument="--parallel" type="boolean" label="Run in parallel where available?" truevalue="--parallel" falsevalue="" checked="true"/> 43 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
44 <conditional name="phylogenetic"> 44 <conditional name="phylogenetic">
45 <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available"> 45 <param argument="--nonphylogenetic_diversity" type="select" label="Apply non-phylogenetic alpha (chao1 and observed_otus) and beta (bray_curtis) diversity calculations?" help="This is useful if, for example, when working with non-amplicon BIOM tables, or if a reliable tree is not available">
46 <option value="--nonphylogenetic_diversity">Yes</option> 46 <option value="--nonphylogenetic_diversity">Yes</option>
47 <option value="" selected="true">No</option> 47 <option value="" selected="true">No</option>
48 </param> 48 </param>
49 <when value=""> 49 <when value="">
50 <param argument="--tree_fp" type="data" format="txt" label="Tree file"/> 50 <param argument="--tree_fp" type="data" format="txt" label="Tree file"/>
51 </when> 51 </when>
52 <when value="--nonphylogenetic_diversity"/> 52 <when value="--nonphylogenetic_diversity"/>
53 </conditional> 53 </conditional>
54 <param argument="--suppress_taxa_summary" type="boolean" label="Suppress generation of taxa summary plots?" truevalue="--suppress_taxa_summary" falsevalue="" checked="False"/> 54 <param argument="--suppress_taxa_summary" type="boolean" truevalue="--suppress_taxa_summary" falsevalue="" checked="false" label="Suppress generation of taxa summary plots?"/>
55 <param argument="--suppress_beta_diversity" type="boolean" label="Suppress beta diversity analyses?" truevalue="--suppress_beta_diversity" falsevalue="" checked="False"/> 55 <param argument="--suppress_beta_diversity" type="boolean" truevalue="--suppress_beta_diversity" falsevalue="" checked="false" label="Suppress beta diversity analyses?"/>
56 <param argument="--suppress_alpha_diversity" type="boolean" label="Suppress alpha diversity analyses?" truevalue="--suppress_alpha_diversity" falsevalue="" checked="False"/> 56 <param argument="--suppress_alpha_diversity" type="boolean" truevalue="--suppress_alpha_diversity" falsevalue="" checked="false" label="Suppress alpha diversity analyses?"/>
57 <param argument="--suppress_group_significance" type="boolean" label="Suppress OTU/category significance analysis?" truevalue="--suppress_group_significance" falsevalue="" checked="False"/> 57 <param argument="--suppress_group_significance" type="boolean" truevalue="--suppress_group_significance" falsevalue="" checked="false" label="Suppress OTU/category significance analysis?"/>
58 <param argument="--categories" type="text" value="" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed" optional="true"/> 58 <param argument="--categories" type="text" value="" optional="true" label="Metadata category or categories to compare for categorical analyses (optional)" help="The column headers in the mapping file should be passed as a comma-separated list. By default, no categorical analyses are performed"/>
59 </inputs> 59 </inputs>
60 <outputs> 60 <outputs>
61 <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/> 61 <data name="html_report" format="html" label="${tool.name} on ${on_string}: Core diversity report"/>
62 </outputs> 62 </outputs>
63 <tests> 63 <tests>