| Previous changeset 1:b5489f81c2fa (2023-10-18) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 22916ed24dfb8452c8142e5d6b282d0e931af91f |
|
modified:
macros.xml pepquery2.xml |
| b |
| diff -r b5489f81c2fa -r c32806a80862 macros.xml --- a/macros.xml Wed Oct 18 06:40:40 2023 +0000 +++ b/macros.xml Wed May 08 17:12:21 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.0.2</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="citations"> <citations> <citation type="doi">10.1101/gr.235028.118</citation> @@ -20,7 +20,7 @@ #end if #end def #def clean($name1) - #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf|raw)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) + #set $name_clean = $re.sub('[^\w\-_]', '_', $re.sub('(?i)[.](fa|fas|fasta|imzml|mzml|mzxml|mgf)$','', $re.sub('.*/','', $name1.rstrip('.gz')))) #return $name_clean #end def #def ln_name($ds) @@ -31,8 +31,6 @@ #set $ext = ".mzXML" #else if $ds.is_of_type('mgf') #set $ext = ".mgf" - #else if $ds.is_of_type('thermo.raw') - #set $ext = ".raw" #else if $ds.is_of_type('fasta') #set $ext = ".fasta" #end if |
| b |
| diff -r b5489f81c2fa -r c32806a80862 pepquery2.xml --- a/pepquery2.xml Wed Oct 18 06:40:40 2023 +0000 +++ b/pepquery2.xml Wed May 08 17:12:21 2024 +0000 |
| b |
| @@ -159,7 +159,7 @@ </param> <when value="novel"/> <when value="known"> - <param name="decoy" argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/> + <param argument="-decoy" type="boolean" truevalue="-decoy" falsevalue="" checked="false" label="Identity the decoy version of the selected target protein"/> </when> </conditional> <section name="req_inputs" title="Input Data" expanded="true"> @@ -257,7 +257,7 @@ <option value="public">public proteomics data repositories</option> </param> <when value="history"> - <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml,thermo.raw" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML,Thermo RAW" /> + <param name="spectrum_files" argument="-ms" type="data" format="mgf,mzml,mzxml" label="Spectrum File" help="Spectrum file used for identification, formats: MGF,mzML,mzXML" /> </when> <when value="indexed"> <param name="index" argument="-ms" type="data" format="txt" label="PepQuery Index" help="" /> @@ -276,7 +276,7 @@ </when> </conditional> - <param name="indexType" argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" > + <param argument="-indexType" type="select" optional="true" label="Report Spectrum Scan as" help="Default: index" > <option value="1">index (1-based) in MGF</option> <option value="2">spectrum title in MGF</option> </param> @@ -307,7 +307,7 @@ <param name="max_mods" argument="-maxVar" type="integer" label="Max Modifications" value="" min="0" max="10" optional="true" help="Max number of variable modifications Default: 3" /> <param name="unmodified" argument="-hc" type="boolean" truevalue="-hc" falsevalue="" checked="false" label="Use more stringent criterion for unrestricted modification searching" help="TRUE: score(UMS)>=score(targetPSM); FALSE: score(UMS)>score(targetPSM)" /> - <param name="aa" argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." /> + <param argument="-aa" type="boolean" truevalue="-aa" falsevalue="" checked="false" label="Consider amino acid substitution modifications?" help="Whether or not to consider aa substitution modifications when perform modification filtering." /> </section> <section name="digestion" title="Digestion" expanded="false"> @@ -369,7 +369,7 @@ <option value="ptm_detail.txt">ptm_detail.txt</option> <option value="ms_index">MS/MS Index</option> </param> - <param name="fast" argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." /> + <param argument="-fast" type="boolean" truevalue="-fast" falsevalue="" checked="false" label="Use fast mode for searching" help="In fast mode, only one better match from reference peptide-based competitive filtering steps will be returned. A peptide identified or not is not affected by this setting. For most applications, fast mode will speed up the analysis." /> </inputs> <outputs> <data name="log_txt" format="txt" from_work_dir="log.txt" label="${tool.name} on ${on_string}: log.txt"> |