Mercurial > repos > jjohnson > qiime

diff alpha_rarefaction.xml @ 0:e5c3175506b7 default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial tool configs for qiime, most need work.
author Jim Johnson <jj@umn.edu>
date Sun, 17 Jul 2011 10:30:11 -0500
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_rarefaction.xml	Sun Jul 17 10:30:11 2011 -0500
@@ -0,0 +1,108 @@
+<tool id="alpha_rarefaction" name="alpha_rarefaction" version="1.2.0">
+ <description>A workflow script for performing alpha rarefaction</description>
+ <requirements>
+  <requirement type="binary">alpha_rarefaction.py</requirement>
+ </requirements>
+ <command interpreter="python">
+  qiime_wrapper.py
+  --galaxy_summary_html='$output_html'
+  --galaxy_outputdir='$output_html.extra_files_path'
+  --galaxy_summary_template='$output_template'
+  ## --galaxy_datasets='^rarefaction_plots.html$:'$output_html
+  alpha_rarefaction.py
+  --otu_table_fp=$otu_table_fp
+  --mapping_fp=$mapping_fp
+  --output_dir=$output_html.extra_files_path
+  #if $parameter.source == 'hist':
+   --parameter_fp=$parameter_fp
+  #else:
+   --parameter_fp=$parameter_generated
+  #end if
+  --num_steps=$num_steps
+  $force
+  $print_only
+  $parallel
+  #if $tree_fp != None and $tree_fp.__str__ != 'None':
+   --tree_fp=$tree_fp
+  #end if
+ </command>
+ <inputs>
+  <param name="otu_table_fp" type="data" format="qiimeotutable" label="otu_table_fp"
+   help="the input otu table [REQUIRED]"/>
+  <param name="mapping_fp" type="data" format="qiimemapping" label="mapping_fp"
+   help="path to the mapping file [REQUIRED]"/>
+  <conditional name="parameter">
+   <param name="source" type="select" label="Parameters from" help="">
+    <option value="hist">Your History</option>
+    <option value="build">Build a Parameter file</option>
+   </param>
+   <when value="hist">
+    <param name="parameter_fp" type="data" format="qiimeparams" label="parameter_fp"
+     help="path to the parameter file [REQUIRED]"/>
+   </when> <!-- hist -->
+   <when value="build">
+   <!--
+	params['alpha_diversity']['metrics'].split(',')
+	params['multiple_rarefactions']
+	params['parallel'])
+	params['alpha_diversity'])
+	params['collate_alpha']
+	params['make_rarefaction_plots']
+    multiple_rarefactions.py
+     min seqs/sample
+     max seqs/sample
+     step
+     depth    sequences per sample to subsample
+     num-reps
+     lineages_included 
+     keep_empty_otus
+    alpha_diversity.py
+    collate_alpha.py
+    make_rarefaction_plots.py
+   -->
+   </when> <!-- build -->
+  </conditional> <!-- parameter -->
+  <param name="num_steps" type="integer" value="10" label="num_steps"
+   help="number of steps (or rarefied OTU table sizes) to make between min and max counts [default: 10]"/>
+  <param name="force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="force"
+   help="Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: ('NO', 'DEFAULT')]"/>
+  <param name="print_only" type="boolean" truevalue="--print_only" falsevalue="" checked="false" label="print_only"
+   help="Print the commands but don't call them -- useful for debugging [default: False]"/>
+  <param name="parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="parallel"
+   help="Run in parallel where available [default: False]"/>
+  <param name="tree_fp" type="data" format="txt" optional="true" label="tree_fp"
+   help="path to the tree file [default: REQUIRED for phylogenetic measures]"/>
+ </inputs>
+ <configfiles>
+  <configfile name="parameter_generated">
+alpha_diversity:metrics	chao1,observed_species,PD_whole_tree
+multiple_rarefactions_even_depth:num-reps	20
+parallel:jobs_to_start	2
+parallel:retain_temp_files	False
+parallel:seconds_to_sleep	60
+collate_alpha:example_path
+make_rarefaction_plots:imagetype	png
+make_rarefaction_plots:resolution	75
+make_rarefaction_plots:background_color	white
+make_rarefaction_plots:prefs_path
+  </configfile>
+  <configfile name="output_template">
+<![CDATA[
+<html>
+<body>
+<a href="rarefaction_plots.html">rarefaction_plots.html</a>
+</body>
+</html>
+]]>
+  </configfile>
+ </configfiles>
+ <outputs>
+  <data format="html" name="output_html" label="alpha_rarefaction_plots"/>
+ </outputs>
+ <tests>
+ </tests>
+ <help>
+  
+ </help>
+</tool>
+