Mercurial > repos > iracooke > protk_proteogenomics

annotate filter_psms.xml @ 3:86fd1757f102 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
author iracooke
date Mon, 21 Dec 2015 23:43:55 -0500
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86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
iracooke
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1 <tool id="filter_psms" name="Filter PSMs" version="1.0.0">
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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2 <description>Select PSMs in a pepXML file matching criteria</description>
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4 <requirements>
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5 <requirement type="package" version="1.4">protk</requirement>
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6 </requirements>
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8 <command>
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9 filter_psms.rb
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11 '
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12 $first_expression
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13 #for $expression in $expressions:
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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14 ,${expression.expression}
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15 #end for
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16 '
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18 $pepxml_file
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20 --attribute $attribute
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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22 $check_alt
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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24 $reverse
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26 -o $output
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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29 </command>
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31 <stdio>
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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32 <exit_code range="1:" level="fatal" description="Failure" />
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33 </stdio>
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35 <inputs>
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37 <param name="pepxml_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Proteomics Search Results" help="A pepXML file"/>
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40 <param name="first_expression" type="text" size="40" value="decoy_" label="Expression">
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41 <sanitizer>
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42 <valid initial="string.printable">
86fd1757f102 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98
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43 <remove value="&apos;"/>
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44 </valid>
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45 <mapping initial="none">
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46 <add source="&apos;" target="__sq__"/>
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47 </mapping>
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48 </sanitizer>
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49 </param>
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51 <repeat name="expressions" title="Expressions to Match against" help="These can include regular expressions">
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52 <param name="expression" type="text" size="40" value="decoy_" label="Expression">
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53 <sanitizer>
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54 <valid initial="string.printable">
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55 <remove value="&apos;"/>
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56 </valid>
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57 <mapping initial="none">
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58 <add source="&apos;" target="__sq__"/>
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59 </mapping>
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60 </sanitizer>
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61 </param>
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62 </repeat>
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64 <param name="attribute" type="text" size="40" value="protein" label="Attribute to use for filtering" help="Must be an attribute of a pepXML search_hit node. For example, protein or peptide">
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65 <sanitizer>
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66 <valid initial="string.printable">
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67 <remove value="&apos;"/>
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68 </valid>
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69 <mapping initial="none">
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70 <add source="&apos;" target="__sq__"/>
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71 </mapping>
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72 </sanitizer>
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73 </param>
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75 <param name="reverse" type="boolean" label="Keep mismatches instead of matches" truevalue="--reject" falsevalue="" />
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77 <param name="check_alt" type="boolean" label="Check alternative_protein entries" truevalue="--check-alternatives" falsevalue="" help="Also apply the search filter to the protein attribute of alternative_protein entries under each search_hit. A match to any counts as a match."/>
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79 </inputs>
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81 <outputs>
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82 <data format="pepxml" name="output" />
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83 </outputs>
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85
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86 <help>
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87
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88 **What it does**
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89
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90 Filters PSMs in a pepXML file keeping only those that match filtering criteria
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91
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92 ----
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94 **References**
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95
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96
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97 </help>
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99 </tool>