Mercurial > repos > computational-metabolomics > mspurity_purityx

comparison purityX.xml @ 0:a141be614e76 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author computational-metabolomics
date Wed, 27 Nov 2019 12:41:53 -0500
parents
children b16952cc06d2
comparison
equal deleted inserted replaced
-1:000000000000 0:a141be614e76
1 <tool id="mspurity_purityx" name="msPurity.purityX" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
2 <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset.
3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 Rscript '$__tool_directory__/purityX.R'
10 --xset_path='$xset'
11 --out_dir='.'
12 --minOffset=$minoffset
13 --maxOffset=$maxoffset
14 --singleFile=$singleFile
15 --purityType=$purityType
16 --cores=\${GALAXY_SLOTS:-4}
17 #if $xgroups.xgroups == "choose"
18 --xgroups='$xgroups.xgroups_value'
19 #end if
20 --camera_xcms=$camera_xcms
21 #if $camera_xcms == "camera"
22 --rdata_name=xa
23 #else
24 --rdata_name=xset
25 #end if
26 --iwNorm=$iw_norm
27 --ilim=$ilim
28 #if $isotopes.isotopes == "exclude_default"
29 --exclude_isotopes
30 #elif $isotopes.isotopes == "user"
31 --exclude_isotopes
32 --isotope_matrix='$isotopes.im'
33 #end if
34 #if $file_load_conditional.file_load_select == 'yes'
35 --galaxy_files='
36 #for $i in $file_load_conditional.input
37 $i,
38 #end for
39 '
40 #end if
41 #if $file_load_conditional.file_load_select == 'yes'
42 --files='
43 #for $i in $file_load_conditional.input
44 $i.name,
45 #end for
46 '
47 #end if
48
49 #if $choose_class_cond.choose_class== 'choose'
50 --choose_class=$choose_class_cond.class
51 #end if
52 #if $ignore_files_cond.ignore_files_choice== 'choose'
53 --ignore_files=$ignore_files_cond.ignore_files
54 #end if
55
56 #if $raw_rt_columns
57 --rtraw_columns
58 #end if
59
60
61 ]]></command>
62 <inputs>
63
64 <param argument="--xset" type="data" format="rdata"
65 help="xcmsSet object saved as an RData file"/>
66 <expand macro="offsets" />
67 <expand macro="general_params" />
68 <param argument="--singleFile" type="integer" label="singleFile" value="0"
69 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
70 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
71
72 <conditional name="choose_class_cond">
73 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
74 <option value="choose">Choose class</option>
75 <option value="all" selected="true">calculate average across all classes</option>
76 </param>
77 <when value="all">
78 </when>
79 <when value="choose">
80 <param argument="--class" type="text" label="Choose class"
81 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
82 i.e. xset@phenoData). An average will across all the choosen classes." />
83 </when>
84 </conditional>
85
86 <conditional name="ignore_files_cond">
87 <param name="ignore_files_choice" type="select" label="Ignore files?" >
88 <option value="choose">Choose files to ignore from calculation</option>
89 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
90 </param>
91 <when value="none">
92 </when>
93 <when value="choose">
94 <param argument="--ignore_files" type="text" label="ignore files"
95 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
96 </when>
97 </conditional>
98
99
100 <conditional name="xgroups">
101 <param name="xgroups" type="select" label="xgroups" >
102 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
103 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
104 </param>
105 <when value="choose">
106 <param name="xgroups_value" type="text" label="xgroup ids"
107 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
108 </when>
109 <when value="all"/>
110 </conditional>
111
112
113 <param argument="--purityType" type="select" label="Method of averaging purity"
114 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
115 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
116 <option value="purityFWHMmean" >FWHM mean</option>
117 <option value="purityFWmedian" >FW median</option>
118 <option value="purityFWmean" >FW mean</option>
119 </param>
120
121 <expand macro="camera_xcms" />
122
123 <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
124 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
125 the retention time correction tracking is slightly different to the other correction methods. To ensure
126 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
127 any retention time correction."/>
128
129 <expand macro="fileload" />
130
131 </inputs>
132 <outputs>
133 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
134 from_work_dir="purityX.tsv" />
135 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
136 from_work_dir="purityX.rdata" />
137 </outputs>
138 <tests>
139 <test>
140 <conditional name="file_load_conditional">
141 <param name="file_load_select" value="yes"/>
142 <param name="input" >
143 <collection type="list">
144 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
145 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
146 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
147 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
148 </collection>
149 </param>
150 </conditional>
151 <conditional name="xgroups">
152 <param name="xgroups" value="choose"/>
153 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
154 </conditional>
155 <param name="iw_norm" value="QE5" />
156 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
157 <output name="purityX_tsv" value="purityX_output.tsv" />
158 <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
159 </test>
160 </tests>
161 <help><![CDATA[
162
163 ===================================================================
164 Calculate anticipated precursor ion purity from LC-MS XCMS dataset
165 ===================================================================
166 -----------
167 Description
168 -----------
169
170 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
171 XCMS determined features
172
173 --------------
174 Output example
175 --------------
176 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
177 metrics regarding the anticipated precursor ion purity.
178
179 ============= ============= ============= ================ ================ ================ ================ ================ ================
180 grpid mean median sd stde RSD pknm i mz
181 ============= ============= ============= ================ ================ ================ ================ ================ ================
182 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
183 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
184 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
185 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
186 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
187 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
188 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
189 ============= ============= ============= ================ ================ ================ ================ ================ ================
190
191
192
193 ]]></help>
194 <expand macro="citations" />
195 </tool>