Mercurial > repos > rjmw > dimspy_process_scans
comparison process_scans.xml @ 1:769165c75514 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 42331bc61ea07d75f88007e5a2c65eaf9e811f06
| author | rjmw |
|---|---|
| date | Wed, 30 May 2018 09:20:20 -0400 |
| parents | d129e75a31d9 |
| children |
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| 0:d129e75a31d9 | 1:769165c75514 |
|---|---|
| 2 <description> - Read, filter and average MS scans</description> | 2 <description> - Read, filter and average MS scans</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
| 7 <expand macro="stdio" /> | 7 <command detect_errors="exit_code"> |
| 8 <command><![CDATA[ | 8 <![CDATA[ |
| 9 #if $input.format == "data_collection" | 9 #if $input.format == "data_collection" |
| 10 #for $fn in $input.source | 10 #for $fn in $input.source |
| 11 #if str( $fn ).endswith(".dat") | 11 #if str( $fn ).endswith(".dat") |
| 12 ln -s "$fn" "$fn.name" | 12 ln -s '$fn' '$fn.name' |
| 13 && | 13 && |
| 14 #end if | 14 #end if |
| 15 #end for | 15 #end for |
| 16 #elif $input.format == "single_file" | 16 #elif $input.format == "single_file" |
| 17 #if str( $input.source ).endswith(".dat") | 17 #if str( $input.source ).endswith(".dat") |
| 18 ln -s "$input.source" "$input.source.name" | 18 ln -s '$input.source' '$input.source.name' |
| 19 && | 19 && |
| 20 #end if | 20 #end if |
| 21 #end if | 21 #end if |
| 22 dimspy process-scans | 22 dimspy process-scans |
| 23 #if $input.format == "data_collection" | 23 #if $input.format == "data_collection" |
| 24 #for $fn in $input.source | 24 #for $fn in $input.source |
| 25 --input "$fn.name" | 25 --input '$fn.name' |
| 26 #end for | 26 #end for |
| 27 #elif $input.format == "single_file" | 27 #elif $input.format == "single_file" |
| 28 --input "$input.source.name" | 28 --input '$input.source.name' |
| 29 #elif $input.format == "library" | 29 #elif $input.format == "library" |
| 30 --input $__app__.config.user_library_import_dir/$__user_email__/$input.source | 30 --input '$__app__.config.user_library_import_dir/$__user_email__/$input.source' |
| 31 #else | 31 #else |
| 32 --input "$input.source" | 32 --input '$input.source' |
| 33 #end if | 33 #end if |
| 34 --output "$hdf5_file_out" | 34 --output '$hdf5_file_out' |
| 35 #if $filelist | 35 #if $filelist |
| 36 --filelist "$filelist" | 36 --filelist '$filelist' |
| 37 #end if | 37 #end if |
| 38 --function-noise $function_noise | 38 --function-noise $function_noise |
| 39 --snr-threshold $snr_threshold | 39 --snr-threshold $snr_threshold |
| 40 --ppm $mults.ppm | 40 --ppm $mults.ppm |
| 41 --min_scans $mults.min_scans | 41 --min_scans $mults.min_scans |
| 49 #end if | 49 #end if |
| 50 #if $adv.skip_stitching | 50 #if $adv.skip_stitching |
| 51 --skip-stitching | 51 --skip-stitching |
| 52 #end if | 52 #end if |
| 53 #if float($adv.ringing_threshold) > 0.0 | 53 #if float($adv.ringing_threshold) > 0.0 |
| 54 --ringing_threshold $adv.ringing_threshold | 54 --ringing-threshold $adv.ringing_threshold |
| 55 #end if | 55 #end if |
| 56 #for $mzr in $adv.remove_mz_range | 56 #for $mzr in $adv.remove_mz_range |
| 57 --remove-mz-range $mzr.start $mzr.end | 57 --remove-mz-range $mzr.start $mzr.end |
| 58 #end for | 58 #end for |
| 59 #if $scan_events.filter == "true" | 59 #if $scan_events.filter == "true" |
| 63 #elif $scan_events.incl_excl == "exclude" | 63 #elif $scan_events.incl_excl == "exclude" |
| 64 --exclude-scan-events $se.start $se.end $se.scan_type | 64 --exclude-scan-events $se.start $se.end $se.scan_type |
| 65 #end if | 65 #end if |
| 66 #end for | 66 #end for |
| 67 #end if | 67 #end if |
| 68 --report "$report" | 68 --report '$report' |
| 69 && | 69 && |
| 70 dimspy hdf5-pls-to-txt | 70 dimspy hdf5-pls-to-txt |
| 71 --input "$hdf5_file_out" | 71 --input '$hdf5_file_out' |
| 72 --output . | 72 --output . |
| 73 --delimiter $delimiter | 73 --delimiter $delimiter |
| 74 ]]></command> | 74 ]]> |
| 75 </command> | |
| 75 <inputs> | 76 <inputs> |
| 76 <conditional name="input"> | 77 <conditional name="input"> |
| 77 <param name="format" type="select" label="Choose the source for the dataset" > | 78 <param name="format" type="select" label="Choose the source for the dataset" > |
| 78 <option value="zip_file" selected="true">Zip file from your History containing *.mzML files</option> | 79 <option value="zip_file" selected="true">Zip file from your History containing *.mzML files</option> |
| 79 <option value="library">Library directory name</option> | 80 <option value="library">Library directory name</option> |