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