# HG changeset patch # User galaxyp # Date 1606752027 0 # Node ID 052798dd73dd15634e69d34ff63bf41b160f4c57 # Parent 06747cba568597ec2dd6367c0635f052194aaafb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 7aa618964e95528ed59eea299701e65ccacae877" diff -r 06747cba5685 -r 052798dd73dd msconvert.xml --- a/msconvert.xml Mon Nov 16 17:24:27 2020 +0000 +++ b/msconvert.xml Mon Nov 30 16:00:27 2020 +0000 @@ -1,4 +1,4 @@ - + Convert and/or filter mass spectrometry files msconvert_macros.xml @@ -6,6 +6,9 @@ chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@ + + + diff -r 06747cba5685 -r 052798dd73dd msconvert_macros.xml --- a/msconvert_macros.xml Mon Nov 16 17:24:27 2020 +0000 +++ b/msconvert_macros.xml Mon Nov 30 16:00:27 2020 +0000 @@ -1,7 +1,6 @@ - 3.0.19052 - @VERSION@-089e81090 - + 3.0.20287 + @VERSION@-769529fa4 /dev/null; echo \$?) && + CAN_SUDO=\$(sudo -n -l > /dev/null 2> /dev/null; echo $?) && if [ "\$CAN_SUDO" -eq "0" ]; then - uid=`id -u` && - gid=`id -g` && - WINE="wine64_anyuser"; + uid=`id -u` && + gid=`id -g` && + WINE="wine64_anyuser"; else - WINE="wine64" && - ## create a writable copy of wine prefix (since copying fails for some html - ## stderr and exit code is swallowed) - export WINEPREFIX=\$(mktemp -d) && - (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true); + WINE="wine64" && + ## create a writable copy of wine prefix (since copying fails for some html + ## stderr and exit code is swallowed) + export WINEPREFIX=\$(mktemp -d) && + (cp -a /wineprefix64/* \$WINEPREFIX 2> /dev/null || true); fi && \$WINE msconvert ${inputmask} @@ -214,21 +212,25 @@ #if $general_options.multi_run_output.do_multi_run_output == 'false': --outfile '${os.path.splitext($basename)[0]}' - && - if [ "\$CAN_SUDO" -eq "0" ]; then - sudo chown \$uid:\$gid 'outputs/${os.path.splitext($basename)[0]}.${output_type}' && - sudo mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; - else - mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}'; - fi + #end if + && + if [ "\$CAN_SUDO" -eq "0" ]; then + sudo chown -R \$uid:\$gid './'; + fi + #if $general_options.multi_run_output.do_multi_run_output == 'false': + && mv 'outputs/${os.path.splitext($basename)[0]}.${output_type}' '${output}' #else - && ls -la outputs/ + ## make mzML and mzXML extensions lower case (the Galaxy data type is ) otherwise detetion of the file + ## TODO this won't be necessay from Galaxy 21.01 https://github.com/galaxyproject/galaxy/pull/10803 + #if $output_type == 'mzML' or $output_type == 'mzXML' + && find outputs/ -name "*.$output_type" | xargs -I "FILE" sh -c 'mv FILE outputs/\$(basename FILE .$output_type).#echo str($output_type).lower() + ## a newline is needed after `#echo ...` therefore the `;'` on the next line +;' + #end if #end if #if $data_processing.precursor_refinement.use_mzrefinement - && if [ "\$CAN_SUDO" -ne "0" ]; then - mv '$output_refinement_name' '$output_refinement'; - fi + && mv '$output_refinement_name' '$output_refinement'; #end if ]]> @@ -543,13 +545,13 @@ - + - + @@ -558,47 +560,47 @@ - + - + - + - + - + - + - + - + - + - + - + - + @@ -606,10 +608,10 @@ - + - + @@ -617,56 +619,56 @@ - + - + - - + + - + - - + + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -737,12 +739,12 @@ - - + + - + @@ -752,10 +754,10 @@ - + - + @@ -767,10 +769,10 @@ - + - + @@ -781,10 +783,10 @@ - + - + @@ -794,20 +796,20 @@ - + - + - + - + @@ -815,26 +817,26 @@ - + - + - + - + - + - + @@ -844,44 +846,44 @@ - + - + - + - + - + - + - + - + - + - + @@ -891,7 +893,7 @@ - +