Mercurial > repos > galaxyp > fastg2protlib
comparison fastg2protlib-peptides.xml @ 0:25dd9931d6b1 draft default tip
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fastg2protlib commit e777bdb1d28b1ffee75cb1a8ad782a50c10a5358"
| author | galaxyp |
|---|---|
| date | Fri, 07 Aug 2020 10:16:55 +0000 |
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| children |
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| -1:000000000000 | 0:25dd9931d6b1 |
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| 1 <tool id="fastg2protlib-peptides" name="FASTG2Protlib-Peptides" version="@VERSION@"> | |
| 2 <macros> | |
| 3 <import>macros.xml</import> | |
| 4 </macros> | |
| 5 <description>Generate FASTA from FASTG</description> | |
| 6 <expand macro="pkg_requirement" /> | |
| 7 <command detect_errors="exit_code"> | |
| 8 <![CDATA[ | |
| 9 python '$__tool_directory__/application.py' | |
| 10 -m $min_peptide_length | |
| 11 -p $min_protein_length | |
| 12 -c $cleavage | |
| 13 -d 'results.db' | |
| 14 -l $show_plots | |
| 15 '$fastg_file' | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param name="fastg_file" type="data" format="fastg" label="FASTG file" /> | |
| 20 <param name="cleavage" type="select" label="Peptide Cleavage"> | |
| 21 <option value="trypsin" selected="true">Trypsin</option> | |
| 22 <expand macro="cleavages" /> | |
| 23 </param> | |
| 24 <param name="min_protein_length" type="integer" value="55" label="Minimum Protein Length in Amino Acids" /> | |
| 25 <param name="min_peptide_length" type="integer" value="8" label="Minimum Peptide Length in Amino Acids" /> | |
| 26 <param name="show_plots" type="boolean" checked="true" label="Create Diagnostic Plots" /> | |
| 27 </inputs> | |
| 28 <outputs> | |
| 29 <data name="peptide_fasta" format="txt" from_work_dir="peptide.fasta" label="${on_string} Peptides from FASTG" /> | |
| 30 <data name="results_db" format="sqlite" from_work_dir="results.db" label="${on_string} Results DB" /> | |
| 31 <data name="aa_count_plot" format="png" from_work_dir="aa_count_chart.png" label="${on_string} AA Count Plot"> | |
| 32 <filter>show_plots == True</filter> | |
| 33 </data> | |
| 34 <data name="fastg_length_plot" format="png" from_work_dir="fastg_seq_lengths.png" label="${on_string} FASTG Sequence Length Plot"> | |
| 35 <filter>show_plots == True</filter> | |
| 36 </data> | |
| 37 <data name="protein_length_plot" format="png" from_work_dir="protein_seq_lengths.png" label="${on_string} Protein Sequence Length Plot"> | |
| 38 <filter>show_plots == True</filter> | |
| 39 </data> | |
| 40 <data name="gc_pct_plot" format="png" from_work_dir="gc_pct.png" label="${on_string} GC Percent Plot"> | |
| 41 <filter>show_plots == True</filter> | |
| 42 </data> | |
| 43 </outputs> | |
| 44 <tests> | |
| 45 <test> | |
| 46 <param name="fastg_file" value="two.fastg" /> | |
| 47 <param name="cleavage" value="trypsin" /> | |
| 48 <param name="min_protein_length" value="20" /> | |
| 49 <param name="min_peptide_length" value="8" /> | |
| 50 <param name="show_plots" value="false" /> | |
| 51 <output name="peptide_fasta"> | |
| 52 <assert_contents> | |
| 53 <has_text text="IFLPFSTHSR" /> | |
| 54 </assert_contents> | |
| 55 </output> | |
| 56 </test> | |
| 57 </tests> | |
| 58 <expand macro="help-text" /> | |
| 59 </tool> |