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comparison purityA.xml @ 15:8398f2a364ee draft default tip

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
author tomnl
date Wed, 27 Nov 2019 12:36:24 +0000
parents a6f519dff5a8
children
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14:f3429f48ae0a 15:8398f2a364ee
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <stdio> 9 <command detect_errors="exit_code"><![CDATA[
10 <exit_code range="1:" /> 10 Rscript '$__tool_directory__/purityA.R'
11 </stdio> 11 --out_dir='.'
12 <command interpreter="Rscript"><![CDATA[ 12
13 purityA.R 13 --mzML_files='
14 --out_dir=. 14 #for $i in $source
15 #if $mzML_data.format == "mzML_files"
16 --mzML_files='
17 #for $i in $mzML_data.source
18 $i, 15 $i,
19 #end for 16 #end for
20 ' 17 '
21 --galaxy_names=' 18 --galaxy_names='
22 #for $i in $mzML_data.source 19 #for $i in $source
23 $i.name, 20 $i.name,
24 #end for 21 #end for
25 ' 22 '
26 #elif $mzML_data.format == "library" 23
27 --mzML_files $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source 24 #if $offsets.offsets == 'user'
28 #end if
29 #if $offsets.offsets == 'user'
30 --minOffset=$minoffset 25 --minOffset=$minoffset
31 --maxOffset=$maxoffset 26 --maxOffset=$maxoffset
32 #end if 27 #end if
33 28
34 --iwNorm=$iw_norm 29 --iwNorm=$iw_norm
46 41
47 #if $isotopes.isotopes == "exclude_default" 42 #if $isotopes.isotopes == "exclude_default"
48 --exclude_isotopes 43 --exclude_isotopes
49 #elif $isotopes.isotopes == "user" 44 #elif $isotopes.isotopes == "user"
50 --exclude_isotopes 45 --exclude_isotopes
51 --isotope_matrix=$isotopes.im 46 --isotope_matrix='$isotopes.im'
52 #end if 47 #end if
53 48
54 --ppmInterp "$ppmInterp" 49 --ppmInterp $ppmInterp
55 50
56 ]]></command> 51 ]]></command>
57 <inputs> 52 <inputs>
58 53 <param name="source" type="data" multiple="true" format="mzml" label="*.mzML file" >
59 <conditional name="mzML_data">
60 <param name="format" type="select" label="Choose the source for the dataset" >
61 <option value="mzML_files" selected="true">.mzML files to check purity from</option>
62 <option value="library">Library directory name (to be used with dimspy workflows) or path to
63 to an individual .mzML file</option>
64 </param>
65 <when value="mzML_files">
66 <param name="source" type="data_collection" format="mzml" label="*.mzML files" >
67 <validator type="empty_field" /> 54 <validator type="empty_field" />
68 </param> 55 </param>
69 </when> 56 <param argument="--mostIntense" type="boolean" checked="true"
70 <when value="library">
71 <param name="source" type="text"
72 size="40" label="Library directory containing *.mzml files
73 or path to an individual *.mzML">
74 <validator type="empty_field" />
75 </param>
76 </when>
77 </conditional>
78
79 <param name="mostIntense" type="boolean" checked="true" argument="--mostIntense"
80 label="Use most intense peak within isolation window for precursor?" 57 label="Use most intense peak within isolation window for precursor?"
81 help="If yes, this will ignore the recorded precursor within the mzML file and use 58 help="If yes, this will ignore the recorded precursor within the mzML file and use
82 use the most intense peak within the isolation window to calculate the precursor ion purity"/> 59 use the most intense peak within the isolation window to calculate the precursor ion purity"/>
83 60
84 <param name="nearest" type="boolean" checked="true" argument="--nearest" 61 <param argument="--nearest" type="boolean" checked="true"
85 label="Use nearest full scan to determine precursor?" 62 label="Use nearest full scan to determine precursor?"
86 help="If TRUE, this will use the neareset full scan to the fragmentation scan to determine what the m/z value 63 help="If TRUE, this will use the neareset full scan to the fragmentation scan to determine what the m/z value
87 is of the precursor"/> 64 is of the precursor"/>
88 65
89 <param name="ppmInterp" type="float" label="Interpolation PPM" value="7" argument='--ppmInterp' 66 <param argument="--ppmInterp" type="float" label="Interpolation PPM" min="0" value="7"
90 help="Set the ppm tolerance for the precursor ion purity interpolation. 67 help="Set the ppm tolerance for the precursor ion purity interpolation.
91 i.e. the ppm tolerence between the precursor ion found in the neighbouring scans. The closest match 68 i.e. the ppm tolerence between the precursor ion found in the neighbouring scans. The closest match
92 within the window will be used for the interpolation"/> 69 within the window will be used for the interpolation"/>
93
94 70
95 <conditional name="offsets"> 71 <conditional name="offsets">
96 <param name="offsets" type="select" label="offsets" > 72 <param name="offsets" type="select" label="offsets" >
97 <option value="auto" selected="true">Uses offsets determined in the mzML file</option> 73 <option value="auto" selected="true">Uses offsets determined in the mzML file</option>
98 <option value="user">User supplied offset values</option> 74 <option value="user">User supplied offset values</option>
99 </param> 75 </param>
100 <when value="user"> 76 <when value="user">
101 <expand macro="offsets" /> 77 <expand macro="offsets" />
102 </when> 78 </when>
103 <when value="auto"> 79 <when value="auto"/>
104 </when>
105 80
106 </conditional> 81 </conditional>
107 82
108 <expand macro="general_params" /> 83 <expand macro="general_params" />
109
110 84
111 </inputs> 85 </inputs>
112 <outputs> 86 <outputs>
113 <data name="purityA_output_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" 87 <data name="purityA_output_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
114 from_work_dir="purityA_output.tsv" /> 88 from_work_dir="purityA_output.tsv" />
115 <data name="purityA_output_rdata" format="rdata" label="${tool.name} on ${on_string}: RData" 89 <data name="purityA_output_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
116 from_work_dir="purityA_output.RData" /> 90 from_work_dir="purityA_output.RData" />
117 </outputs> 91 </outputs>
118 <tests> 92 <tests>
119 <test> 93 <test>
120 <conditional name="mzML_data"> 94 <param name="source" value="LCMSMS_2.mzML,LCMSMS_1.mzML,LCMS_2.mzML,LCMS_1.mzML" ftype="mzml" />
121 <param name="format" value="mzML_files"/>
122 <param name="source" >
123 <collection type="list">
124 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
125 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
126 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
127 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
128 </collection>
129 </param>
130 </conditional>
131 <output name="purityA_output_tsv" value="purityA_output.tsv" /> 95 <output name="purityA_output_tsv" value="purityA_output.tsv" />
132 <output name="purityA_output_rdata" value="purityA_output.RData" ftype="rdata" compare="sim_size"/> 96 <output name="purityA_output_rdata" value="purityA_output.RData" ftype="rdata" compare="sim_size"/>
133 </test> 97 </test>
134 </tests> 98 </tests>
135 99