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comparison alpha_rarefaction.xml @ 5:0a097fc6e5a6 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 07:13:54 -0400
parents d493a0d5d5f5
children 9023dcdccf72
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4:b56b7dcd6229 5:0a097fc6e5a6
1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0">
2 <description>A workflow script for performing alpha rarefaction</description> 2 <description>(alpha_rarefaction)</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>alpha_rarefaction.py --version</version_command> 7 <version_command>alpha_rarefaction.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
12 alpha_rarefaction.py
13 --otu_table_fp '$otu_table_fp'
14 --mapping_fp '$mapping_fp'
15 -o alpha_rarefaction
16 #if $parameter_fp
17 --parameter_fp '$parameter_fp'
18 #end if
19 --num_steps '$num_steps'
20 $parallel
21 -O "\${GALAXY_SLOTS:-4}"
22 #if $tree_fp
23 --tree_fp '$tree_fp'
24 #end if
25 --min_rare_depth '$min_rare_depth'
26 #if $max_rare_depth
27 --max_rare_depth '$max_rare_depth'
28 #end if
29 $retain_intermediate_files
30 11
31 && mkdir -p $alpha_rarefaction_plots.files_path 12 alpha_rarefaction.py
32 && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots 13 --otu_table_fp '$otu_table_fp'
33 && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path 14 --mapping_fp '$mapping_fp'
15 -o alpha_rarefaction
16 #if $parameter_fp
17 --parameter_fp '$parameter_fp'
18 #end if
19 --num_steps '$num_steps'
20 $parallel
21 -O "\${GALAXY_SLOTS:-4}"
22 #if $tree_fp
23 --tree_fp '$tree_fp'
24 #end if
25 --min_rare_depth '$min_rare_depth'
26 #if $max_rare_depth
27 --max_rare_depth '$max_rare_depth'
28 #end if
29 $retain_intermediate_files
30
31 && mkdir -p $alpha_rarefaction_plots.files_path
32 && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
33 && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
34 ]]></command> 34 ]]></command>
35 <inputs> 35 <inputs>
36 <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/> 36 <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
37 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/> 37 <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
38 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/> 38 <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
39 <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/> 39 <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/>
40 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/> 40 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="true" label="Run in parallel where available?"/>
41 <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="True" label="Tree file (optional)" help="Required for phylogenetic measures"/> 41 <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="true" label="Tree file (optional)" help="Required for phylogenetic measures"/>
42 <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/> 42 <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
43 <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/> 43 <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/>
44 <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/> 44 <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="true" label="Retain intermediate files?"/>
45 </inputs> 45 </inputs>
46 <outputs> 46 <outputs>
47 <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/> 47 <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
48 <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information"> 48 <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information">
49 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/> 49 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/>