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annotate metaquantome_filter.xml @ 1:47bfbd6597d0 draft

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author galaxyp
date Wed, 05 Dec 2018 14:37:17 -0500
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children 28180bbb8fe4
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1 <tool id="metaquantome_filter" name="MetaQuantome Filter" version="@VERSION@.0">
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2 <description>for quality, redundancy, and sample coverage</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 @MAKE_SAMPS_TSV@
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9 metaquantome filter
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10 @COMMON_PARAMS@
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11 --expand_file '$expand_file'
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12 --min_peptides $min_peptides
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13 #if $min_pep_nsamp:
1
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14 #set $nsamp = max(int($min_peptides),int($min_pep_nsamp))
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15 --min_pep_nsamp $nsamp
0
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16 #else
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17 --min_pep_nsamp all
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18 #end if
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19 --min_children_non_leaf $min_children_non_leaf
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20 #if $min_child_nsamp:
1
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21 #set $nsamp = max($min_peptides,$min_child_nsamp)
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22 --min_child_nsamp $nsamp
0
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23 #else
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24 --min_child_nsamp all
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25 #end if
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26 --qthreshold $qthreshold
1
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27 --outfile='$outfile'
0
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28 ]]></command>
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29 <inputs>
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30 <expand macro="common_params"/>
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31 <param argument="--expand_file" type="data" format="tabular" label="metaquantome expand file"
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32 help=""/>
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33 <param argument="--min_peptides" type="integer" value="0" min="0" label="min_peptides">
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34 <help>
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35 Used for filtering to well-supported annotations. The
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36 number of peptides providing evidence for a term is
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37 the number of peptides directly annotated with that
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38 term plus the number of peptides annotated with any of
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39 its descendants. Terms with a number of peptides
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40 greater than or equal to min_peptides are retained.
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41 The default is 0.
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42 </help>
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43 </param>
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44 <param argument="--min_pep_nsamp" type="integer" value="" min="0" optional="true" label="min_pep_nsamp">
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45 <help>
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46 Number of samples per group that must meet or exceed
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47 min_peptides. Default is 'all'.
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48 </help>
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49 </param>
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50 <param argument="--min_children_non_leaf" type="integer" value="0" min="0" label="min_children_non_leaf">
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51 <help>
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52 Used for filtering to informative annotations. A term
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53 is retained if it has a number of children greater
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54 than or equal to min_children_non_leaf. The default is 0.
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55 </help>
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56 </param>
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57 <param argument="--min_child_nsamp" type="integer" value="" min="0" optional="true" label="min_child_nsamp">
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58 <help>
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59 Number of samples per group that must meet or exceed
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60 min_children_nsamp. Default is 'all'.
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61 </help>
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62 </param>
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63 <param argument="--qthreshold" type="integer" value="3" min="0" label="qthreshold">
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64 <help>
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65 Minimum number of intensities in each sample group.
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66 Any functional/taxonomic term with lower number of
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67 per-group intensities will be filtered out. The
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68 default is 3, because this is the minimum number for
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69 t-tests.
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70 </help>
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71 </param>
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72
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73 <expand macro="output_samples_choice"/>
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74 </inputs>
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75 <outputs>
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76 <data format="tabular" name="outfile" label="${tool.name} on ${on_string} filtered"/>
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77 <expand macro="output_samples"/>
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78 </outputs>
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79 <help><![CDATA[
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80 TODO: Fill in help.
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81 ]]></help>
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82 <expand macro="citations" />
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83 </tool>