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comparison purityX.xml @ 0:ddda01fb1503 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2948ce35fa7fffe5a64711cb30be971031e79019-dirty
author tomnl
date Fri, 24 May 2019 09:15:53 -0400
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children e4d251e0b7eb
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-1:000000000000 0:ddda01fb1503
1 <tool id="mspurity_purityx" name="msPurity.purityX" version="0.2.0">
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
8 <expand macro="requirements" />
9
10 <stdio>
11 <exit_code range="1:" />
12 </stdio>
13 <command interpreter="Rscript"><![CDATA[
14 purityX.R
15 --xset_path=$xset
16 --out_dir=.
17 --minOffset=$minoffset
18 --maxOffset=$maxoffset
19 --singleFile=$singleFile
20 --purityType=$purityType
21 --cores=\${GALAXY_SLOTS:-4}
22 #if $xgroups.xgroups == "choose"
23 --xgroups=$xgroups.xgroups_value
24 #end if
25 --camera_xcms=$camera_xcms
26 #if $camera_xcms == "camera"
27 --rdata_name=xa
28 #else
29 --rdata_name=xset
30 #end if
31 --iwNorm=$iw_norm
32 --ilim=$ilim
33 #if $isotopes.isotopes == "exclude_default"
34 --exclude_isotopes
35 #elif $isotopes.isotopes == "user"
36 --exclude_isotopes
37 --isotope_matrix=$isotopes.im
38 #end if
39 #if $file_load_conditional.file_load_select == 'yes'
40 --galaxy_files='
41 #for $i in $file_load_conditional.input
42 $i,
43 #end for
44 '
45 #end if
46 #if $file_load_conditional.file_load_select == 'yes'
47 --files='
48 #for $i in $file_load_conditional.input
49 $i.name,
50 #end for
51 '
52 #end if
53
54 #if $choose_class_cond.choose_class== 'choose'
55 --choose_class=$choose_class_cond.class
56 #end if
57 #if $ignore_files_cond.ignore_files_choice== 'choose'
58 --ignore_files=$ignore_files_cond.ignore_files
59 #end if
60
61 #if $raw_rt_columns
62 --rtraw_columns
63 #end if
64
65
66 ]]></command>
67 <inputs>
68
69 <param type="data" name="xset" format="rdata"
70 help="xcmsSet object saved as an RData file"/>
71 <expand macro="offsets" />
72 <expand macro="general_params" />
73 <param name="singleFile" type="integer" label="singleFile" value="0"
74 help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
75 Uses the index of the files in xcmsSet object. If zero this is ignored"/>
76
77 <conditional name="choose_class_cond">
78 <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
79 <option value="choose">Choose class</option>
80 <option value="all" selected="true">calculate average across all classes</option>
81 </param>
82 <when value="all">
83 </when>
84 <when value="choose">
85 <param name="class" type="text" label="Choose class"
86 help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
87 i.e. xset@phenoData). An average will across all the choosen classes." />
88 </when>
89 </conditional>
90
91 <conditional name="ignore_files_cond">
92 <param name="ignore_files_choice" type="select" label="Ignore files?" >
93 <option value="choose">Choose files to ignore from calculation</option>
94 <option value="none" selected="true" >Include all files of selected classes in calculation</option>
95 </param>
96 <when value="none">
97 </when>
98 <when value="choose">
99 <param name="ignore_files" type="text" label="ignore files"
100 help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML" />
101 </when>
102 </conditional>
103
104
105 <conditional name="xgroups">
106 <param name="xgroups" type="select" label="xgroups" >
107 <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
108 <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
109 </param>
110 <when value="all">
111 </when>
112 <when value="choose">
113 <param name="xgroups_value" type="text" label="xgroup ids"
114 help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4" />
115 </when>
116 </conditional>
117
118
119 <param name="purityType" type="select" label="Method of averaging purity"
120 help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
121 <option value="purityFWHMmedian" selected="true" >FWHM median</option>
122 <option value="purityFWHMmean" >FWHM mean</option>
123 <option value="purityFWmedian" >FW median</option>
124 <option value="purityFWmean" >FW mean</option>
125 </param>
126
127 <expand macro="camera_xcms" />
128
129 <param name="raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
130 help="Only applicable when using retention time correction with obiwarp. When obiwarp is used
131 the retention time correction tracking is slightly different to the other correction methods. To ensure
132 correct tracking with obiwarp an additional tool (track_rt_raw) should be performed prior to
133 any retention time correction."/>
134
135 <expand macro="fileload" />
136
137 </inputs>
138 <outputs>
139 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
140 from_work_dir="purityX.tsv" />
141 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
142 from_work_dir="purityX.rdata" />
143 </outputs>
144 <tests>
145 <test>
146 <conditional name="file_load_conditional">
147 <param name="file_load_select" value="yes"/>
148 <param name="input" >
149 <collection type="list">
150 <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
151 <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
152 <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
153 <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
154 </collection>
155 </param>
156 </conditional>
157 <conditional name="xgroups">
158 <param name="xgroups" value="choose"/>
159 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
160 </conditional>
161 <param name="iw_norm" value="QE5" />
162 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
163 <output name="purityX_tsv" value="purityX_output.tsv" />
164 <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/>
165 </test>
166 </tests>
167 <help><![CDATA[
168
169 ===================================================================
170 Calculate anticipated precursor ion purity from LC-MS XCMS dataset
171 ===================================================================
172 -----------
173 Description
174 -----------
175
176 Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
177 XCMS determined features
178
179 --------------
180 Output example
181 --------------
182 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
183 metrics regarding the anticipated precursor ion purity.
184
185 ============= ============= ============= ================ ================ ================ ================ ================ ================
186 grpid mean median sd stde RSD pknm i mz
187 ============= ============= ============= ================ ================ ================ ================ ================ ================
188 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
189 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
190 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
191 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
192 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
193 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
194 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
195 ============= ============= ============= ================ ================ ================ ================ ================ ================
196
197
198
199 ]]></help>
200 <expand macro="citations" />
201 </tool>