Mercurial > repos > cpt > cpt_psm_prep
comparison cpt_psm_prep/cpt_psm_0_prep.xml @ 0:e4de0a0e90c8 draft
Uploaded
| author | cpt |
|---|---|
| date | Tue, 05 Jul 2022 05:38:34 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:e4de0a0e90c8 |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <tool id="PSM.Prep" name="PSM Prep" version="1.94.2"> | |
| 3 <description>prepares data for the PSM Plotter</description> | |
| 4 <version_command>perl cpt_psm_0_prep.pl --version</version_command> | |
| 5 <stdio> | |
| 6 <exit_code range="1:" level="fatal"/> | |
| 7 </stdio> | |
| 8 <requirements> | |
| 9 <requirement type="package" version="5.22.1">perl</requirement> | |
| 10 <requirement type="package">perl-bioperl</requirement> | |
| 11 <requirement type="package">perl-moose</requirement> | |
| 12 <requirement type="package">perl-ipc-run</requirement> | |
| 13 <requirement type="package">perl-getopt-long-descriptive</requirement> | |
| 14 </requirements> | |
| 15 <command detect_errors="aggressive"><![CDATA[ | |
| 16 perl -Mlib=$__tool_directory__/lib $__tool_directory__/cpt_psm_0_prep.pl | |
| 17 --galaxy | |
| 18 --outfile_supporting $__new_file_path__ | |
| 19 #for $item in $repeat_file: | |
| 20 --file "${item.file}" | |
| 21 #end for | |
| 22 | |
| 23 --cpt_psm_object "${cpt_psm_object}" | |
| 24 | |
| 25 --cpt_psm_object_files_path "${cpt_psm_object.files_path}" | |
| 26 | |
| 27 --cpt_psm_object_format "${cpt_psm_object_format}" | |
| 28 | |
| 29 --cpt_psm_object_id "${cpt_psm_object.id}" | |
| 30 | |
| 31 ]]></command> | |
| 32 <inputs> | |
| 33 <repeat name="repeat_file" title="File"> | |
| 34 <param name="file" help="Input file" optional="False" label="file" type="data"/> | |
| 35 </repeat> | |
| 36 <param name="cpt_psm_object_format" help="Output PSM Object" optional="False" label="Format of cpt_psm_object" type="select"> | |
| 37 <option value="TXT" selected="True">TXT</option> | |
| 38 <option value="CONF">CONF</option> | |
| 39 </param> | |
| 40 </inputs> | |
| 41 <outputs> | |
| 42 <data name="cpt_psm_object" format="TXT"> | |
| 43 <change_format> | |
| 44 <when input="cpt_psm_object_format" value="TXT" format="txt"/> | |
| 45 <when input="cpt_psm_object_format" value="CONF" format="txt"/> | |
| 46 </change_format> | |
| 47 </data> | |
| 48 </outputs> | |
| 49 <help>NAME | |
| 50 ==== | |
| 51 | |
| 52 PSM Prep | |
| 53 | |
| 54 DESCRIPTION | |
| 55 =========== | |
| 56 | |
| 57 This tool takes in 2 or more GenBank files, blasts, and prepares data | |
| 58 structures for use in the companion tool: PSM Plotter. Select as many | |
| 59 (multi)-gbk files as you *might* want to plot. Once this tool is done, | |
| 60 you can select any subset of those to plot then. | |
| 61 </help> | |
| 62 <tests/> | |
| 63 </tool> |