Mercurial > repos > galaxyp > metaquantome
view metaquantome_filter.xml @ 3:28180bbb8fe4 draft
planemo upload commit 3762c462ff510cccd856f4ccd7fb87c44ad9b4e7
author | galaxyp |
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date | Thu, 06 Dec 2018 08:50:19 -0500 |
parents | 47bfbd6597d0 |
children | 80ce9ca55697 |
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<tool id="metaquantome_filter" name="MetaQuantome Filter" version="@VERSION@.0"> <description>for quality, redundancy, and sample coverage</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @MAKE_SAMPS_TSV@ metaquantome filter @COMMON_PARAMS@ --expand_file '$expand_file' --min_peptides $min_peptides #if $min_pep_nsamp: #set $nsamp = max(int($min_peptides),int($min_pep_nsamp)) --min_pep_nsamp $nsamp #else --min_pep_nsamp all #end if --min_children_non_leaf $min_children_non_leaf #if $min_child_nsamp: #set $nsamp = max($min_peptides,$min_child_nsamp) --min_child_nsamp $nsamp #else --min_child_nsamp all #end if --qthreshold $qthreshold --outfile='$outfile' ]]></command> <inputs> <expand macro="common_params"/> <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file" help=""/> <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides"> <help> Used for filtering to well-supported annotations. The number of peptides providing evidence for a term is the number of peptides directly annotated with that term plus the number of peptides annotated with any of its descendants. Terms with a number of peptides greater than or equal to min_peptides are retained. The default is 0. </help> </param> <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp"> <help> Number of samples per group that must meet or exceed min_peptides. Default is 'all'. </help> </param> <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf"> <help> Used for filtering to informative annotations. A term is retained if it has a number of children greater than or equal to min_children_non_leaf. The default is 0. </help> </param> <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp"> <help> Number of samples per group that must meet or exceed min_children_nsamp. Default is 'all'. </help> </param> <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold"> <help> Minimum number of intensities in each sample group. Any functional/taxonomic term with lower number of per-group intensities will be filtered out. The default is 3, because this is the minimum number for t-tests. </help> </param> <expand macro="output_samples_choice"/> </inputs> <outputs> <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/> <expand macro="output_samples"/> </outputs> <tests> <test> <param name="expand_file" value="go_expanded.tab" ftype="tabular"/> <param name="mode" value="f" /> <param name="ontology" value="go" /> <param name="samps_src" value="build" /> <repeat name="samps"> <param name="group_name" value="s1"/> <param name="col_names" value="int1,int2,int3"/> </repeat> <repeat name="samps"> <param name="group_name" value="s2"/> <param name="col_names" value="int4,int5,int6"/> </repeat> <param name="min_peptides" value="1" /> <param name="min_pep_nsamp" value="1" /> <param name="min_children_non_leaf" value="2" /> <param name="min_child_nsamp" value="1" /> <param name="qthreshold" value="2" /> <output name="outfile" file="go_filtered.tab" ftype="tabular"/> </test> </tests> <help><![CDATA[ TODO: Fill in help. ]]></help> <expand macro="citations" /> </tool>