Mercurial > repos > galaxyp > hardklor
changeset 6:f416698530c3 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/hardklor commit 44c3e37a12f60b01521d3e3f18b7f16664f954cc"
| author | galaxyp |
|---|---|
| date | Tue, 07 Apr 2020 07:22:58 +0000 |
| parents | b236958c496e |
| children | |
| files | hardklor.py hardklor.xml kronik.xml |
| diffstat | 3 files changed, 29 insertions(+), 16 deletions(-) [+] |
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--- a/hardklor.py Sat Aug 19 08:00:08 2017 -0400 +++ b/hardklor.py Tue Apr 07 07:22:58 2020 +0000 @@ -10,10 +10,10 @@ CONFIG_FILE = 'hk.conf' extension_lookup = { - 'mzml' : 'mzML', - 'mzxml' : 'mzXML', - 'ms1' : 'MS1', - } + 'mzml': 'mzML', + 'mzxml': 'mzXML', + 'ms1': 'MS1', +} # input: ms1_ext = sys.argv[1] @@ -33,7 +33,7 @@ ms1_ext = extension_lookup[ms1_ext] linkname = 'ms1_dsetlink.{0}'.format(ms1_ext) os.symlink(ms1_file, linkname) - ms1_file = linkname + ms1_file = linkname # load template and dump to config file with open(config_load) as fp: @@ -53,7 +53,7 @@ maxfeat=options['maxfeat'], inputfile=ms1_file, outputfile=output_file, - ) +) with open(CONFIG_FILE, 'w') as fp: fp.write(config_to_dump)
--- a/hardklor.xml Sat Aug 19 08:00:08 2017 -0400 +++ b/hardklor.xml Tue Apr 07 07:22:58 2020 +0000 @@ -1,16 +1,29 @@ -<tool id="hardklor" name="Hardklor" version="2.30.1"> +<tool id="hardklor" name="Hardklor" version="2.30.1+galaxy1"> <description>identification of features from mass spectra</description> <requirements> <requirement type="package" version="2.3.0">hardklor</requirement> + <requirement type="package" version="3.7">python</requirement> </requirements> - <stdio> - <exit_code range="1:" level="fatal"/> - </stdio> - <command>python $__tool_directory__/hardklor.py "$ms1_in.extension" "$ms1_in" - "$output" -charge_algo=$cdm -resolution=$res -centroided=$centroided -instrument=$instrument -algorithm=$algorithm -mincharge=$chMin - -maxcharge=$chMax -mslvl=$mslvl -correlation=$corr -depth=$depth -sensitivity=$sens -maxfeat=$maxfeat</command> + <command detect_errors="exit_code"><![CDATA[ +python '$__tool_directory__/hardklor.py' + '$ms1_in.extension' + '$ms1_in' + '$output' + -charge_algo=$cdm + -resolution=$res + -centroided=$centroided + -instrument=$instrument + -algorithm=$algorithm + -mincharge=$chMin + -maxcharge=$chMax + -mslvl=$mslvl + -correlation=$corr + -depth=$depth + -sensitivity=$sens + -maxfeat=$maxfeat + ]]></command> <inputs> - <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra " /> + <param name="ms1_in" type="data" format="mzml" label="MS1 files with precursor spectra" /> <param name="res" type="integer" value="60000" label="Spectral resolution at 400m/z" /> <param name="centroided" type="select" display="radio" label="Centroided data?"> <option value="0" selected="true">No</option>
--- a/kronik.xml Sat Aug 19 08:00:08 2017 -0400 +++ b/kronik.xml Tue Apr 07 07:22:58 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="kronik" name="Kronik" version="2.20"> +<tool id="kronik" name="Kronik" version="2.20+galaxy1"> <description>processes Hardklor features to find peptides by chromatographic profiling</description> <requirements> <requirement type="package" version="2.20">kronik</requirement> @@ -6,7 +6,7 @@ <stdio> <exit_code range="1:" level="fatal" description="Error occurred while running Kronik"/> </stdio> - <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p "$inputfile" "$output"</command> + <command>kronik -c $c -d $d -g $g -m $m -n $n -p $p '$inputfile' '$output'</command> <inputs> <param name="inputfile" type="data" format="hardklor" label="Hardklör isotope distributions" /> <param name="c" type="integer" value="5" label="Contaminant threshold in minutes" help="Peptides persisting for longer than this value are excluded" />