Mercurial > repos > computational-metabolomics > sirius_csifingerid

comparison sirius_csifingerid.xml @ 4:8fb51147d15e draft

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"planemo upload for repository https://github.com/computational-metabolomics/sirius_csifingerid_galaxy commit fdeefc696443bc3aadf08d4df7226cb6f91d0388"
author computational-metabolomics
date Fri, 04 Feb 2022 10:09:40 +0000
parents 4cbfd3d0a4c4
children 57c4e7421085
comparison
equal deleted inserted replaced
3:4cbfd3d0a4c4 4:8fb51147d15e
1 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID" 1 <tool id="sirius_csifingerid" name="SIRIUS-CSI:FingerID"
2 version="4.9.8+galaxy0" profile="21.01"> 2 version="4.9.8+galaxy0" profile="19.05">
3 <description>is used to identify metabolites using single and 3 <description>is used to identify metabolites using single and
4 tandem mass spectrometry</description> 4 tandem mass spectrometry</description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="4.9.8"> 6 <requirement type="package" version="4.9.8">
7 sirius-csifingerid</requirement> 7 sirius-csifingerid</requirement>
59 <inputs> 59 <inputs>
60 <param name="input" argument="--input_pth" type="data" format="msp" 60 <param name="input" argument="--input_pth" type="data" format="msp"
61 label="MSP file (output from Create MSP tool)" /> 61 label="MSP file (output from Create MSP tool)" />
62 <param argument="--database" type="select" 62 <param argument="--database" type="select"
63 label="Select SIRIUS-CSI:FingerID Database" > 63 label="Select SIRIUS-CSI:FingerID Database" >
64 <option value="PubChem" >PubChem</option> 64 <option value="PUBCHEM" >PubChem</option>
65 <option value="hmdb">HMDB</option> 65 <option value="HMDB">HMDB</option>
66 <option value="kegg">KEGG</option> 66 <option value="KEGG">KEGG</option>
67 <option value="knapsack">KNApSAcK</option> 67 <option value="KNAPSACK">KNApSAcK</option>
68 <option value="biocyc">BioCyc</option> 68 <option value="BIOCYC">BioCyc</option>
69 <option selected="true" value="bio">Bio (all biological)</option> 69 <option selected="true" value="BIO">Bio (all biological)</option>
70 <option value="all">All use all databases</option> 70 <option value="ALL">All (use all databases)</option>
71 </param> 71 </param>
72 <param argument="--ppm_max" type="integer" value="10" min="0" 72 <param argument="--ppm_max" type="integer" value="10" min="0"
73 label="Mass deviation of the fragment peaks in ppm" /> 73 label="Mass deviation of the fragment peaks in ppm" />
74 <param argument="--candidates" type="integer" value="5" min="1" 74 <param argument="--candidates" type="integer" value="5" min="1"
75 label="Maximum number of candidates in the output" /> 75 label="Maximum number of candidates in the output" />
141 141
142 <param argument="--rank_filter" type="integer" value="0" 142 <param argument="--rank_filter" type="integer" value="0"
143 label="Only show the top ranked annotations less than or equal 143 label="Only show the top ranked annotations less than or equal
144 to this value (default to show all annotations)"/> 144 to this value (default to show all annotations)"/>
145 145
146 <param argument="--confidence_filter" type="integer" value="0" 146 <param argument="--confidence_filter" type="float" value="0"
147 label="Only show annotations greater than or or equal 147 label="Only show annotations greater than or or equal
148 to this value (default to show all annotations)"/> 148 to this value (default to show all annotations)"/>
149 149
150 <param argument="--backwards_compatible" type="boolean" checked="false" 150 <param argument="--backwards_compatible" type="boolean" checked="false"
151 label="Makes the outputs compatible with annotation workflows that used the old output from 151 label="Makes the outputs compatible with annotation workflows that used the old output from
152 SIRIUS:CSI:FingerID v4.0.1"/> 152 SIRIUS-CSI:FingerID v4.0.1"/>
153 </inputs> 153 </inputs>
154 <outputs> 154 <outputs>
155 <data name="canopus_results" format="tsv" label="${tool.name} on ${on_string}: CANOPUS" 155 <data name="canopus_results" format="tsv" label="${tool.name} on ${on_string}: CANOPUS"
156 from_work_dir="canopus_all_summary.tsv"/> 156 from_work_dir="canopus_all_summary.tsv"/>
157 <data name="annotation_results" format="tsv" label="${tool.name} on ${on_string}: Annotations" 157 <data name="annotation_results" format="tsv" label="${tool.name} on ${on_string}: Annotations"
207 <param name="profile" value="orbitrap"/> 207 <param name="profile" value="orbitrap"/>
208 <param name="backwards_compatible" value="--backwards_compatible"/> 208 <param name="backwards_compatible" value="--backwards_compatible"/>
209 <output name="annotation_results" file="bc_annotation_CCMSLIB00000578155_result.tsv"/> 209 <output name="annotation_results" file="bc_annotation_CCMSLIB00000578155_result.tsv"/>
210 <output name="canopus_results" file="bc_canopus_CCMSLIB00000578155_result.tsv"/> 210 <output name="canopus_results" file="bc_canopus_CCMSLIB00000578155_result.tsv"/>
211 </test> 211 </test>
212 <test>
213 <!-- Test confidence filter -->
214 <param name="input" value="generic.msp" ftype="msp"/>
215 <param name="confidence_filter" value="0.7"/>
216 <output name="annotation_results" file="cf_annotation_generic_msp_result.tsv"/>
217 <output name="canopus_results" file="cf_canopus_generic_msp_result.tsv"/>
218 </test>
212 </tests> 219 </tests>
213 <help> 220 <help>
214 ---------------- 221 ----------------
215 SIRIUS-FingerID 222 SIRIUS-FingerID
216 ---------------- 223 ----------------