| Previous changeset 4:001e77708ec9 (2013-07-12) Next changeset 6:ffe1dca94595 (2014-02-17) |
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Commit message:
Bjoern: remove unused repository dependency, cleanups |
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modified:
TODO msconvert2.xml msconvert2_raw.xml msconvert3.xml msconvert3_raw.xml msconvert_subset.xml repository_dependencies.xml tool_dependencies.xml version |
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| diff -r 001e77708ec9 -r 08bb52273ae1 TODO --- a/TODO Fri Jul 12 12:45:51 2013 -0400 +++ b/TODO Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,2 +1,1 @@ Add precursorRefine option. -Add peak picking options. \ No newline at end of file |
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| diff -r 001e77708ec9 -r 08bb52273ae1 msconvert2.xml --- a/msconvert2.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/msconvert2.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,8 +1,10 @@ -<tool id="msconvert2" name="msconvert2" version="0.2.0"> +<tool id="msconvert2" name="msconvert2" version="0.2.1"> <!-- BEGIN_VERSION_DEFAULT --> <description>Convert and filter a mass spec peak list</description> <!-- END_VERSION_DEFAULT --> - + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> <command interpreter="python"> #set $ext = $input.ext #if $ext.startswith("m:") @@ -292,11 +294,6 @@ </change_format> </data> </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - <help> **What it does** |
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| diff -r 001e77708ec9 -r 08bb52273ae1 msconvert2_raw.xml --- a/msconvert2_raw.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/msconvert2_raw.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,8 +1,13 @@ -<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.0"> +<tool id="msconvert2_raw" name="msconvert2_raw" version="0.2.1"> <!-- BEGIN_VERSION_RAW --> <description>Convert and filter a Thermo Finnigan RAW file</description> <!-- END_VERSION_RAW --> - + <requirements> + <requirement type="package">proteowizard</requirement> + <!-- BEGIN_VERSION_RAW --> + <requirement type="platform">windows</requirement> + <!-- END_VERSION_RAW --> + </requirements> <command interpreter="python"> #set $ext = $input.ext #if $ext.startswith("m:") @@ -273,14 +278,6 @@ </change_format> </data> </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - <!-- BEGIN_VERSION_RAW --> - <requirement type="platform">windows</requirement> - <!-- END_VERSION_RAW --> - </requirements> - <help> **What it does** |
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| diff -r 001e77708ec9 -r 08bb52273ae1 msconvert3.xml --- a/msconvert3.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/msconvert3.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,8 +1,10 @@ -<tool id="msconvert3" name="msconvert3" version="0.2.0"> +<tool id="msconvert3" name="msconvert3" version="0.2.1"> <!-- BEGIN_VERSION_DEFAULT --> <description>Convert and filter a mass spec peak list</description> <!-- END_VERSION_DEFAULT --> - + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> <command interpreter="python"> #set $ext = $input.ext #if $ext.startswith("m:") @@ -14,7 +16,7 @@ --input_name='${input.display_name}' #end if --output=${output} - ## BEGIN_VERSION_DEFAULT + ## BEGIN_VERSION_DEFAULT --fromextension=$ext ## END_VERSION_DEFAULT @@ -116,7 +118,7 @@ <!-- BEGIN_VERSION_DEFAULT --> <conditional name="type"> - <param name="input_type" type="select" label="Input Type" help="select file type of input data from history- mzml, mzXML, mgf or ms2. then select appropriate input file from drop down menu depending on input in history"> + <param name="input_type" type="select" label="Input Type"> <option value="mzml">mzML</option> <option value="mzxml">mzXML</option> <option value="mgf">mgf</option> @@ -136,7 +138,7 @@ </when> </conditional> <!-- END_VERSION_DEFAULT --> - <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is The standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)."> + <param name="output_type" type="select" label="Output Type"> <option value="mzML">mzML (indexed)</option> <option value="unindexed_mzML">mzML (unindexed)</option> <option value="mzXML">mzXML (indexed)</option> @@ -145,7 +147,7 @@ <option value="ms2">ms2</option> </param> <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (see also peaklist processing)" /> + <param name="filtering_use" type="boolean" label="Use Filtering?" truevalue="true" falsevalue="false" /> <when value="false" /> <when value="true"> <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> @@ -355,11 +357,6 @@ </change_format> </data> </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - <help> **What it does** |
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| diff -r 001e77708ec9 -r 08bb52273ae1 msconvert3_raw.xml --- a/msconvert3_raw.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/msconvert3_raw.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,8 +1,13 @@ -<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.0"> +<tool id="msconvert3_raw" name="msconvert3_raw" version="0.2.1"> <!-- BEGIN_VERSION_RAW --> <description>Convert and filter a Thermo Finnigan RAW file</description> <!-- END_VERSION_RAW --> - + <requirements> + <requirement type="package">proteowizard</requirement> + <!-- BEGIN_VERSION_RAW --> + <requirement type="platform">windows</requirement> + <!-- END_VERSION_RAW --> + </requirements> <command interpreter="python"> #set $ext = $input.ext #if $ext.startswith("m:") @@ -117,7 +122,7 @@ <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input" help="select input file in RAW format"/> <!-- END_VERSION_RAW --> - <param name="output_type" type="select" label="Output Type" help="select file type of output. mzXML is an open, generic XML file type. mzml is the standard file extension for most search engines. ms2 displays a header followed by scan data. mgf is the format for use with MASCOT, OMSSA, ProteinPilot search engines (See MGF Formatter for details)"> + <param name="output_type" type="select" label="Output Type"> <option value="mzML">mzML (indexed)</option> <option value="unindexed_mzML">mzML (unindexed)</option> <option value="mzXML">mzXML (indexed)</option> @@ -126,7 +131,7 @@ <option value="ms2">ms2</option> </param> <conditional name="filtering"> - <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" help="incorporates algorithm that separates noisy peaks from actual ion peaks (also called as peaklist processing)" /> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> <when value="false" /> <when value="true"> <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> @@ -336,14 +341,6 @@ </change_format> </data> </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - <!-- BEGIN_VERSION_RAW --> - <requirement type="platform">windows</requirement> - <!-- END_VERSION_RAW --> - </requirements> - <help> **What it does** @@ -353,21 +350,6 @@ .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html -**Recommended** - -For X!tandem searches: Use mzml format generated from RAW file. - - RAW → mzml - -For ProteinPilot searches: Use MGF format generated from mzml file using MGF formatter. - - RAW → mzml → MGF (ProteinPilot) - -For MaxQuant searches: Use RAW file as an input. - -For OMSSA : Use MGF format generated from mzml file using MGF formatter. - - RAW → mzml → MGF (Mascot) ------ **Citation** |
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| diff -r 001e77708ec9 -r 08bb52273ae1 msconvert_subset.xml --- a/msconvert_subset.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/msconvert_subset.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,5 +1,8 @@ -<tool id="msconvert_subset" name="Subset Peak List" version="0.2.0"> +<tool id="msconvert_subset" name="Subset Peak List" version="0.2.1"> <description>against list of scan numbers or indices.</description> + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> <command interpreter="python"> msconvert_wrapper.py --input=${input} @@ -95,11 +98,6 @@ </change_format> </data> </outputs> - - <requirements> - <requirement type="package">proteowizard</requirement> - </requirements> - <help> </help> </tool> |
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| diff -r 001e77708ec9 -r 08bb52273ae1 repository_dependencies.xml --- a/repository_dependencies.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/repository_dependencies.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,5 +1,4 @@ <?xml version="1.0"?> <repositories description="Required proteomics dependencies."> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="proteomics_datatypes" owner="iracooke" changeset_revision="f74290b136fc" /> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="863462ea0187" /> + <repository name="proteomics_datatypes" owner="iracooke" /> </repositories> |
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| diff -r 001e77708ec9 -r 08bb52273ae1 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 12 12:45:51 2013 -0400 +++ b/tool_dependencies.xml Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="proteowizard" version="3_0_4388"> - <repository toolshed="http://toolshed.g2.bx.psu.edu" name="protk_proteowizard" owner="iracooke" changeset_revision="6ead3520e93a"/> - </package> + <package name="proteowizard" version="3_0_4388"> + <repository name="protk_proteowizard" owner="iracooke"/> + </package> </tool_dependency> |
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| diff -r 001e77708ec9 -r 08bb52273ae1 version --- a/version Fri Jul 12 12:45:51 2013 -0400 +++ b/version Mon Feb 17 08:13:33 2014 -0600 |
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| @@ -1,1 +1,1 @@ -0.2.0 \ No newline at end of file +0.2.1 |