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comparison moff.xml @ 5:a96af68dafb2 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/moFF commit 0bc6529504998425278b15f5b50f94478faede52"
author galaxyp
date Wed, 06 May 2020 14:50:08 -0400
parents 7af419c90f5f
children
comparison
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4:7af419c90f5f 5:a96af68dafb2
1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.0"> 1 <tool id="proteomics_moff" name="moFF" version="@VERSION@.0">
2 <description>extracts MS1 intensities from spectrum files</description> 2 <description>extracts MS1 intensities from spectrum files</description>
3 <macros> 3 <macros>
4 <token name="@VERSION@">2.0.2</token> 4 <token name="@VERSION@">2.0.3</token>
5 <!-- xml macros, used for shared Galaxy parameter inputs --> 5 <!-- xml macros, used for shared Galaxy parameter inputs -->
6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data"> 6 <xml name="ident_input_macro" token_allow_multiple="true" token_input_type="data">
7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff --> 7 <!-- this is exactly the same across all three, except for allowing multiple in MBR and all but not in moff -->
8 <conditional name="ident_input"> 8 <conditional name="ident_input">
9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:"> 9 <param name="input_type_selector" type="select" label="Choose the format for the identification file:">
167 --sample_size $task.match_filter.sample_size 167 --sample_size $task.match_filter.sample_size
168 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering 168 --quantile_thr_filtering $task.match_filter.quantile_thr_filtering
169 #if ($task.match_filter.ptm_file): 169 #if ($task.match_filter.ptm_file):
170 --ptm_file '$task.match_filter.ptm_file' 170 --ptm_file '$task.match_filter.ptm_file'
171 #else: 171 #else:
172 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json' 172 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
173 #end if 173 #end if
174 #end if 174 #end if
175 #if ($task.peptide_summary): 175 #if ($task.peptide_summary):
176 --peptide_summary 176 --peptide_summary
177 #end if 177 #end if
214 --ptm_file '$task.match_filter.ptm_file' 214 --ptm_file '$task.match_filter.ptm_file'
215 #else: 215 #else:
216 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json' 216 --ptm_file '$__tool_directory__/tool-data/ptm_setting_ps.json'
217 #end if 217 #end if
218 #end if 218 #end if
219 219
220 #if $task.peptide_summary: 220 #if $task.peptide_summary:
221 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary' 221 && mv ./out/peptide_summary_intensity_moFF_run.tab '$output_peptide_summary'
222 #end if 222 #end if
223 #end if 223 #end if
224 ]]></command> 224 ]]></command>
253 help="Specify rt window for xic in minutes." /> 253 help="Specify rt window for xic in minutes." />
254 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection" 254 <param argument="--rt_peak_win" type="float" value="1" label="retention time window for apex detection"
255 help="Specify rt window for the peak in minutes." /> 255 help="Specify rt window for the peak in minutes." />
256 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak" 256 <param argument="--rt_peak_win_match" type="float" value="1.2" label="retention time window for the matched peak"
257 help="Specify the retention time window for the matched peak in minutes." /> 257 help="Specify the retention time window for the matched peak in minutes." />
258 <expand macro="filt_matched_peptide"/> 258 <expand macro="filt_matched_peptide"/>
259 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/> 259 <param argument="--peptide_summary" type="boolean" value="true" label="Output the peptide summary?"/>
260 </when> 260 </when>
261 <when value="mbr"> 261 <when value="mbr">
262 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/> 262 <expand macro="ident_input_macro" allow_multiple="false" input_type="data_collection"/>
263 <param argument="--mbr" type="text" value="only" label="moFF workflow" 263 <param argument="--mbr" type="text" value="only" label="moFF workflow"