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comparison ProteinQuantifier.xml @ 0:3d84209d3178 draft

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author bgruening
date Fri, 10 Oct 2014 18:20:03 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
2 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="1.12.0">
3 <description>Compute peptide and protein abundances</description>
4 <macros>
5 <token name="@EXECUTABLE@">ProteinQuantifier</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="stdio"/>
9 <expand macro="requirements"/>
10 <command>ProteinQuantifier
11
12 -in ${param_in}
13 -protxml ${param_protxml}
14 -out ${param_out}
15 -peptide_out ${param_peptide_out}
16 -mzTab_out ${param_mzTab_out}
17 -top ${param_top}
18 -average ${param_average}
19 ${param_include_all}
20 ${param_filter_charge}
21 ${param_ratios}
22 ${param_ratiosSILAC}
23 -threads \${GALAXY_SLOTS:-24}
24 ${param_normalize}
25 ${param_fix_peptides}
26 -format:separator ${param_separator}
27 -format:quoting ${param_quoting}
28 -format:replacement ${param_replacement}
29 </command>
30 <inputs>
31 <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" label="Input file" help="(-in)"/>
32 <param name="param_protxml" type="data" format="idXML" optional="True" label="ProteinProphet results (protXML converted to idXML) for the identification runs that were used to annotate the input.#br#Information about indistinguishable proteins will be used for protein quantification." help="(-protxml)"/>
33 <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top)"/>
34 <param name="param_average" type="select" optional="True" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average)">
35 <option value="median">median</option>
36 <option value="mean">mean</option>
37 <option value="sum">sum</option>
38 </param>
39 <param name="param_include_all" type="boolean" truevalue="-include_all true" falsevalue="-include_all false" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all)"/>
40 <param name="param_filter_charge" type="boolean" truevalue="-filter_charge true" falsevalue="-filter_charge false" checked="false" optional="True" label="Distinguish between charge states of a peptide. For peptides, abundances will be reported separately for each charge;#br#for proteins, abundances will be computed based only on the most prevalent charge of each peptide.#br#By default, abundances are summed over all charge states." help="(-filter_charge)"/>
41 <param name="param_ratios" type="boolean" truevalue="-ratios true" falsevalue="-ratios false" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output. Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) ..." help="(-ratios)"/>
42 <param name="param_ratiosSILAC" type="boolean" truevalue="-ratiosSILAC true" falsevalue="-ratiosSILAC false" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output. Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)" help="(-ratiosSILAC)"/>
43 <param name="param_normalize" type="boolean" truevalue="-consensus:normalize true" falsevalue="-consensus:normalize false" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize)"/>
44 <param name="param_fix_peptides" type="boolean" truevalue="-consensus:fix_peptides true" falsevalue="-consensus:fix_peptides false" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples.#br#With 'top 0', all peptides that occur in every sample are considered.#br#Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected,#br#breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)." help="(-fix_peptides)"/>
45 <param name="param_separator" type="text" size="20" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator)"/>
46 <param name="param_quoting" type="select" optional="True" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes,#br#'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting)">
47 <option value="none">none</option>
48 <option value="double">double</option>
49 <option value="escape">escape</option>
50 </param>
51 <param name="param_replacement" type="text" size="20" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement)"/>
52 </inputs>
53 <outputs>
54 <data name="param_out" label="Output file for protein abundances" format="tabular"/>
55 <data name="param_peptide_out" label="Output file for peptide abundances" format="tabular"/>
56 <data name="param_mzTab_out" label="Export to mzTab.#br#Either 'out', 'peptide_out', or 'mzTab_out' are required. They can be used together." format="tabular"/>
57 </outputs>
58 <help>**What it does**
59
60 Compute peptide and protein abundances
61
62
63 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html
64
65 @REFERENCES@
66 </help>
67 </tool>