| Previous changeset 5:77a18a61aeed (2019-08-30) Next changeset 7:63769c4217a7 (2020-05-04) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/ThermoRawfileParser commit 51cb9a683762b514de76c1654e5e5cac3ff443f8" |
|
modified:
thermo_converter.xml |
| b |
| diff -r 77a18a61aeed -r 2d80c8b2dfc2 thermo_converter.xml --- a/thermo_converter.xml Fri Aug 30 10:28:22 2019 -0400 +++ b/thermo_converter.xml Mon Apr 06 19:00:54 2020 -0400 |
| [ |
| @@ -1,16 +1,12 @@ <tool id="thermo_raw_file_converter" name="Thermo" version="1.1.10"> <description>RAW file converter</description> <requirements> - <requirement type="package" version="1.1.10">ThermoRawFileParser</requirement> + <requirement type="package" version="1.1.10">thermorawfileparser</requirement> </requirements> <command> <![CDATA[ #import re -#set $temp_stderr = "thermo_converter_stderr" - -echo "" > $temp_stderr && - mkdir ./raws_folder && mkdir ./output_folder && #for $input_raw in $input: @@ -22,7 +18,7 @@ #end if #end for -(ThermoRawFileParser.sh +ThermoRawFileParser.sh -d=./raws_folder -o=./output_folder -f=$output_format @@ -33,29 +29,23 @@ $peakpicking_boolean $ignore_instrument_errors_boolean - 2>> $temp_stderr) - - && - #if len($input) == 1: #if $output_format == "0": - mv ./output_folder/input.mgf ./output_file.out && + && mv ./output_folder/input.mgf ./output_file.out #else if $output_format == "1": - mv ./output_folder/input.mzML ./output_file.out && + && mv ./output_folder/input.mzML ./output_file.out #else if $output_format == "2": - mv ./output_folder/input.mzML ./output_file.out && + && mv ./output_folder/input.mzML ./output_file.out #end if #if $output_metadata_selector != "off": #if $output_metadata_selector == "0": - mv ./output_folder/input-metadata.json ./input-metadata.txt && + && mv ./output_folder/input-metadata.json ./input-metadata.txt #else if $output_metadata_selector == "1": - mv ./output_folder/input-metadata.txt ./input-metadata.txt && + && mv ./output_folder/input-metadata.txt ./input-metadata.txt #end if #end if #end if - - cat $temp_stderr 2>&1; ]]> </command> <inputs> @@ -136,17 +126,17 @@ <tests> <!-- Basic test --> <test expect_num_outputs="1"> - <param name="input" value="really_small.raw"/> + <param name="input" value="really_small.raw" ftype="thermo.raw"/> <param name="output_format" value="1"/> <output name="output" file="really_small.mzml" ftype="mzml" compare="sim_size" delta="3000" /> </test> <!-- Testing contents of converted mgf file with txt metadata --> <test expect_num_outputs="2"> - <param name="input" value="really_small.raw"/> + <param name="input" value="really_small.raw" ftype="thermo.raw"/> <param name="output_format" value="0"/> <param name="output_metadata_selector" value="1"/> - <output name="output"> + <output name="output" ftype="mgf"> <assert_contents> <has_text text="SCANS=36"/> <has_text text="RTINSECONDS=73.863181104"/> @@ -176,7 +166,7 @@ <!-- Basic mzml collection test --> <test expect_num_outputs="1"> - <param name="input" value="really_small.raw,really_small_2.raw"/> + <param name="input" value="really_small.raw,really_small_2.raw" ftype="thermo.raw"/> <param name="output_format" value="1"/> <output_collection name="output_mzml_collection" type="list" count="2"/> </test> |