Mercurial > repos > computational-metabolomics > mspurity_purityx

comparison purityX.xml @ 8:b16952cc06d2 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 7e1748612a9f9dce11a9e54ff36752b600e7aea3
author computational-metabolomics
date Wed, 12 Jun 2024 16:02:20 +0000
parents a141be614e76
children
comparison
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7:942e676515fe 8:b16952cc06d2
129 <expand macro="fileload" /> 129 <expand macro="fileload" />
130 130
131 </inputs> 131 </inputs>
132 <outputs> 132 <outputs>
133 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv" 133 <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
134 from_work_dir="purityX.tsv" /> 134 from_work_dir="purityX_output.tsv" />
135 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData" 135 <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
136 from_work_dir="purityX.rdata" /> 136 from_work_dir="purityX_output.RData" />
137 </outputs> 137 </outputs>
138 <tests> 138 <tests>
139 <test> 139 <test>
140 <conditional name="file_load_conditional"> 140 <conditional name="file_load_conditional">
141 <param name="file_load_select" value="yes"/> 141 <param name="file_load_select" value="yes"/>
153 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/> 153 <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
154 </conditional> 154 </conditional>
155 <param name="iw_norm" value="QE5" /> 155 <param name="iw_norm" value="QE5" />
156 <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/> 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" /> 157 <output name="purityX_tsv" value="purityX_output.tsv" />
158 <output name="purityX_rdata" value="purityX_output.Rdata" ftype="rdata" compare="sim_size"/> 158 <output name="purityX_rdata" value="purityX_output.RData" ftype="rdata" compare="sim_size"/>
159 </test> 159 </test>
160 </tests> 160 </tests>
161 <help><![CDATA[ 161 <help><![CDATA[
162 162
163 =================================================================== 163 ===================================================================
175 -------------- 175 --------------
176 Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various 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. 177 metrics regarding the anticipated precursor ion purity.
178 178
179 ============= ============= ============= ================ ================ ================ ================ ================ ================ 179 ============= ============= ============= ================ ================ ================ ================ ================ ================
180 grpid mean median sd stde RSD pknm i mz 180 grpid meanPurity medianPurity sdPurity stdePurity cvPurity pknmPurity i mz
181 ============= ============= ============= ================ ================ ================ ================ ================ ================ 181 ============= ============= ============= ================ ================ ================ ================ ================ ================
182 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758 182 1 1.00 1.00 0.0000 0.0000 0.0000 1 5404920 100.0758
183 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 183 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
184 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084 184 2 0.59 0.57 0.3016 0.1508 50.570 3 8793845 101.0084
185 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 185 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
186 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781 186 3 0.08 0.07 0.0784 0.0164 29.643 4 1526502 100.9781
187 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ---------------- 187 ------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
188 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914 188 4 1.00 1.00 0.0000 0.0000 0.0000 1 42513139 102.0914
189 ============= ============= ============= ================ ================ ================ ================ ================ ================ 189 ============= ============= ============= ================ ================ ================ ================ ================ ================
190 190
191
192 (Note - the additional peakID column is the same as grpid. Included for compatibility with other Galaxy tools)
191 193
192 194
193 ]]></help> 195 ]]></help>
194 <expand macro="citations" /> 196 <expand macro="citations" />
195 </tool> 197 </tool>