| Previous changeset 2:68d8c9e521d7 (2015-10-20) |
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Commit message:
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 864b3f087fff3a7cb18b2c0dd61442c2495e5b98 |
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modified:
tool_dependencies.xml |
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added:
filter_psms.xml |
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| diff -r 68d8c9e521d7 -r 86fd1757f102 filter_psms.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_psms.xml Mon Dec 21 23:43:55 2015 -0500 |
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| @@ -0,0 +1,99 @@ +<tool id="filter_psms" name="Filter PSMs" version="1.0.0"> + <description>Select PSMs in a pepXML file matching criteria</description> + + <requirements> + <requirement type="package" version="1.4">protk</requirement> + </requirements> + + <command> + filter_psms.rb + + ' + $first_expression + #for $expression in $expressions: + ,${expression.expression} + #end for + ' + + $pepxml_file + + --attribute $attribute + + $check_alt + + $reverse + + -o $output + + + </command> + + <stdio> + <exit_code range="1:" level="fatal" description="Failure" /> + </stdio> + + <inputs> + + <param name="pepxml_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Proteomics Search Results" help="A pepXML file"/> + + + <param name="first_expression" type="text" size="40" value="decoy_" label="Expression"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + + <repeat name="expressions" title="Expressions to Match against" help="These can include regular expressions"> + <param name="expression" type="text" size="40" value="decoy_" label="Expression"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + </repeat> + + <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"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + + <param name="reverse" type="boolean" label="Keep mismatches instead of matches" truevalue="--reject" falsevalue="" /> + + <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."/> + + </inputs> + + <outputs> + <data format="pepxml" name="output" /> + </outputs> + + + <help> + +**What it does** + +Filters PSMs in a pepXML file keeping only those that match filtering criteria + +---- + +**References** + + + </help> + +</tool> |
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| diff -r 68d8c9e521d7 -r 86fd1757f102 tool_dependencies.xml --- a/tool_dependencies.xml Tue Oct 20 20:34:50 2015 -0400 +++ b/tool_dependencies.xml Mon Dec 21 23:43:55 2015 -0500 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="protk" version="1.4.3"> - <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="991797b02976" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="blast+" version="2.2.29"> <repository changeset_revision="0b75bc235e70" name="package_blast_plus_2_2_29" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> |