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Changeset 8:26c6706bfb07 (2020-07-25)

Previous changeset 7:63769c4217a7 (2020-05-04) Next changeset 9:92ac8e086317 (2021-02-17)

Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit a502d3fbf1f1ecfca1c9b115beab9d9c0e358fb5"

modified:
thermo_converter.xml

diff -r 63769c4217a7 -r 26c6706bfb07 thermo_converter.xml
--- a/thermo_converter.xml Mon May 04 08:00:32 2020 -0400
+++ b/thermo_converter.xml Sat Jul 25 16:26:42 2020 -0400

[

b'@@ -1,4 +1,4 @@\n-<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3">\n+<tool id="thermo_raw_file_converter" name="Thermo" version="1.2.3+galaxy0">\n <description>RAW file converter</description>\n <requirements>\n <requirement type="package" version="1.2.3">thermorawfileparser</requirement>\n@@ -9,13 +9,9 @@\n \n mkdir ./raws_folder &&\n mkdir ./output_folder &&\n-#for $input_raw in $input:\n- #if len($input) > 1\n- #set $input_name = re.sub(\'[^\\w\\-\\.]\', \'_\',$input_raw.element_identifier.split(\'/\')[-1].replace(".raw", "") + ".raw")\n- ln -s -f \'${input_raw}\' \'./raws_folder/${input_name}\' &&\n- #else:\n- ln -s -f \'${input_raw}\' \'./raws_folder/input.raw\' &&\n- #end if\n+#for $input_raw in $input_files:\n+ #set $input_name = re.sub(\'[^\\w\\-\\.]\', \'_\',$input_raw.element_identifier.split(\'/\')[-1].replace(".raw", "") + ".raw")\n+ ln -s -f \'${input_raw}\' \'./raws_folder/${input_name}\' &&\n #end for\n \n ThermoRawFileParser.sh\n@@ -29,27 +25,10 @@\n $peakpicking_boolean\n $ignore_instrument_errors_boolean\n \n- #if len($input) == 1:\n- #if $output_format == "0":\n- && mv ./output_folder/input.mgf ./output_file.out\n- #else if $output_format == "1":\n- && mv ./output_folder/input.mzML ./output_file.out\n- #else if $output_format == "2":\n- && mv ./output_folder/input.mzML ./output_file.out\n- #end if\n-\n- #if $output_metadata_selector != "off":\n- #if $output_metadata_selector == "0":\n- && mv ./output_folder/input-metadata.json ./input-metadata.txt\n- #else if $output_metadata_selector == "1":\n- && mv ./output_folder/input-metadata.txt ./input-metadata.txt\n- #end if\n- #end if\n- #end if\n ]]>\n </command>\n <inputs>\n- <param name="input" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"\n+ <param name="input_files" type="data" format="thermo.raw" label="Thermo RAW file" help="" multiple="true"\n optional="False" />\n \n <param name="output_format" type="select" label="Output format">\n@@ -76,47 +55,23 @@\n </inputs>\n <outputs>\n \n- \n-\n- <data name="output" format="mzml" from_work_dir="output_file.out" label="${tool.name} on ${on_string}">\n- <filter>(str(input)).count(\',\') == 0</filter> \n- <change_format>\n- <when input="output_format" value="0" format="mgf" />\n- <when input="output_format" value="2" format="txt" />\n- </change_format>\n- </data>\n-\n- <data name="output_metadata" format="txt" label="${tool.name} on ${on_string}: Metadata" from_work_dir="input-metadata.txt">\n- <filter>str(output_metadata_selector) != "off"</filter>\n- <filter>(str(input)).count(\',\') == 0</filter>\n- <change_format>\n- <when input="output_metadata_selector" value="0" format="json" />\n- </change_format>\n- </data>\n-\n- \n-\n- <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF">\n+ <collection name="output_mgf_collection" type="list" label="${tool.name} on ${on_string}: MGF collection">\n <filter>output_format == "0"</filter>\n- <filter>(str(input)).count(\',\') > 0</filter>\n <discover_datasets pattern="(?P<designation>.+)\\.mgf" directory="output_folder" ext="mgf"/>\n </collection>\n \n- <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML">\n+ <collection name="output_mzml_collection" type="list" label="${tool.name} on ${on_string}: mzML collection">\n <filter>output_format == "1"</filter>\n- <'..b' <has_text text="229.2241211 1137.6958007813"/>\n- <has_text text="1577.8967285 1487.9519042969"/>\n- </assert_contents>\n- </output>\n- <output name="output_metadata" ftype="txt">\n- <assert_contents>\n- <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>\n- <has_text text="Instrument name=Orbitrap Fusion"/>\n- <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>\n- <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>\n- <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>\n- <has_text text="Number of scans=101"/>\n- <has_text text="Scan range=1;101"/>\n- <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>\n- <has_text text="Time range=0.89;1.59"/>\n- <has_text text="Mass range=120.0000;2000.0000"/>\n- </assert_contents>\n- </output>\n-\n- </test>\n-\n- \n- <test expect_num_outputs="1">\n- <param name="input" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/>\n- <param name="output_format" value="1"/>\n- <output_collection name="output_mzml_collection" type="list" count="2"/>\n+ <output_collection name="output_mgf_collection" type="list" count="1">\n+ <element name="really_small" ftype="mgf">\n+ <assert_contents>\n+ <has_text text="SCANS=36"/>\n+ <has_text text="RTINSECONDS=73.863181104"/>\n+ <has_text text="PEPMASS=675.248779296875"/>\n+ <has_text text="CHARGE=2+"/>\n+ <has_text text="121.3116455 920.2367553711"/>\n+ <has_text text="229.2241211 1137.6958007813"/>\n+ <has_text text="1577.8967285 1487.9519042969"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ <output_collection name="output_metadata_collection" type="list">\n+ <element name="really_small" ftype="txt">\n+ <assert_contents>\n+ <has_text text="Instrument model=[MS, MS:1000494, Thermo Scientific instrument model, Orbitrap Fusion]"/>\n+ <has_text text="Instrument name=Orbitrap Fusion"/>\n+ <has_text text="Instrument serial number=[MS, MS:1000529, instrument serial number, FSN10188]"/>\n+ <has_text text="Software version=[NCIT, NCIT:C111093, Software Version, 3.1.2412.17]"/>\n+ <has_text text="Mass resolution=[MS, MS:1000011, mass resolution, 0.500]"/>\n+ <has_text text="Number of scans=101"/>\n+ <has_text text="Scan range=1;101"/>\n+ <has_text text="Scan start time=[MS, MS:1000016, scan start time, 0.89]"/>\n+ <has_text text="Time range=0.89;1.59"/>\n+ <has_text text="Mass range=120.0000;2000.0000"/>\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n </test>\n \n \n <test expect_num_outputs="2">\n- <param name="input" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>\n+ <param name="input_files" value="really_small.raw,really_small_2.raw,really_small_3.raw"/>\n <param name="output_format" value="0"/>\n <param name="output_metadata_selector" value="0"/>\n <output_collection name="output_mgf_collection" type="list" count="3"/>\n'