Mercurial > repos > computational-metabolomics > mspurity_purityx
comparison purityX.xml @ 0:a141be614e76 draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
author | computational-metabolomics |
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date | Wed, 27 Nov 2019 12:41:53 -0500 |
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children | b16952cc06d2 |
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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> |