Mercurial > repos > galaxyp > psm_validation
comparison psm_validation.xml @ 0:c634292d3468 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_validation commit 896365c9d6b9fcdcbb9c36e0c81db78c8a4e8dab"
| author | galaxyp |
|---|---|
| date | Thu, 15 Oct 2020 07:44:52 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:c634292d3468 |
|---|---|
| 1 <tool id="psmvalidator" name="PSM-Fragment Validator" version="@VERSION@"> | |
| 2 <macros> | |
| 3 <import>macros.xml</import> | |
| 4 </macros> | |
| 5 <description>Validate PSMs against Ion Fragmentation</description> | |
| 6 <expand macro="pkg_requirement" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 python '$__tool_directory__/application.py' | |
| 10 -d '$mz_db_name' | |
| 11 -p '$peptide_sequences' | |
| 12 #if $neutral_loss_ions: | |
| 13 -n | |
| 14 #end if | |
| 15 #if $internal_ions: | |
| 16 -i | |
| 17 #end if | |
| 18 -b $b_ion_run | |
| 19 -y $y_ion_run | |
| 20 -e $epsilon | |
| 21 #if $b_ion_run < 0: | |
| 22 --test | |
| 23 #end if | |
| 24 ]]> | |
| 25 </command> | |
| 26 <inputs> | |
| 27 <param name="mz_db_name" type="data" format="mz.sqlite" label="MZSQLite DB" /> | |
| 28 <param name="peptide_sequences" type="data" format="tabular" label="Peptide Sequence List" /> | |
| 29 <param name="b_ion_run" type="integer" value="2" label="Consecutive B-Ions" /> | |
| 30 <param name="y_ion_run" type="integer" value="2" label="Consecutive Y-Ions" /> | |
| 31 <param name="neutral_loss_ions" type="boolean" checked="True" label="Use Neutral Loss" /> | |
| 32 <param name="internal_ions" type="boolean" checked="True" label="Use Internals" /> | |
| 33 <param name="epsilon" type="float" value="0.5" label="Epsilon" /> | |
| 34 </inputs> | |
| 35 <outputs> | |
| 36 <data name="html_output" format="html" from_work_dir="index.html" label="PSM Ion Fragementation Report" /> | |
| 37 <data name="text_output" format="tabular" from_work_dir="results.tab" label="Tabular Results" /> | |
| 38 </outputs> | |
| 39 <tests> | |
| 40 <test> | |
| 41 <param name="mz_db_name" value="test.db" /> | |
| 42 <param name="peptide_sequences" value="test-peptides.txt" /> | |
| 43 <param name="b_ion_run" value="-99" /> | |
| 44 <param name="y_ion_run" value="-99" /> | |
| 45 <param name="neutral_loss_ions" value="True" /> | |
| 46 <param name="internal_ions" value="True" /> | |
| 47 <param name="epsilon" value="0.5" /> | |
| 48 <output name="html_output"> | |
| 49 <assert_contents> | |
| 50 <has_text text="success" /> | |
| 51 </assert_contents> | |
| 52 </output> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <expand macro="help-text" /> | |
| 56 </tool> |