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comparison maxquant.xml @ 14:e42225f8a659 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/maxquant commit 9ee3c66acde2e5690b93eca561db78b58df2a07d"
author galaxyp
date Thu, 08 Jul 2021 22:45:35 +0000
parents 181bd6a5f6ce
children 97a7f34fcb6a
comparison
equal deleted inserted replaced
13:181bd6a5f6ce 14:e42225f8a659
30 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files] 30 #set infiles = [$name for $pg in $paramGroups for $name in $pg.files]
31 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles] 31 #set names = [re.sub('@SUBSTITUTION_RX@', '_', str($n.element_identifier)) for $n in $infiles]
32 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names] 32 #set names_with_ext = [($name if ($name).lower().endswith(str($input_opts.ftype)) else $name + str($input_opts.ftype)) for $name in $names]
33 #for $target, $link in zip($infiles, $names_with_ext) 33 #for $target, $link in zip($infiles, $names_with_ext)
34 && 34 &&
35 #if str($input_opts.ftype) == '.thermo.raw':
36 cp '$target' '$link'
37 #else:
35 ln -s '$target' '$link' 38 ln -s '$target' '$link'
39 #end if
36 #end for 40 #end for
37 && 41 &&
38 python3 '$__tool_directory__/create_mqpar.py' 42 python3 '$__tool_directory__/create_mqpar.py'
39 #if $search_opts.template 43 #if $search_opts.template
40 --exp_design='$search_opts.template' 44 --exp_design='$search_opts.template'
452 <option value="2">Semi-specific free C-terminus</option> 456 <option value="2">Semi-specific free C-terminus</option>
453 <option value="3">Semi-specific</option> 457 <option value="3">Semi-specific</option>
454 <option value="4">Unspecific</option> 458 <option value="4">Unspecific</option>
455 <option value="5">No digestion</option> 459 <option value="5">No digestion</option>
456 </param> 460 </param>
457
458 <conditional name="quant_method"> 461 <conditional name="quant_method">
459 <param name="select_quant_method" type="select" label="Quantitation Methods" 462 <param name="select_quant_method" type="select" label="Quantitation Methods"
460 help="Select a method if needed."> 463 help="Select a method if needed.">
461 <option value="">None</option> 464 <option value="">None</option>
462 <option value="lfq">label free quantification</option> 465 <option value="lfq">label free quantification</option>