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author cpt
date Mon, 05 Jun 2023 02:47:24 +0000
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1 <tool id="PSM.Comp" name="PSM Comparison Table" version="1.94">
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2 <description>aligns and lists data from PSM Prep</description>
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3 <version_command>perl cpt_psm_2_gentable.pl --version</version_command>
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4 <stdio>
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5 <exit_code range="1:" level="fatal"/>
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6 </stdio>
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7 <requirements>
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8 <requirement type="package" version="5.22.1">perl</requirement>
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9 <requirement type="package">perl-bioperl</requirement>
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10 <requirement type="package">perl-moose</requirement>
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11 <requirement type="package">perl-ipc-run</requirement>
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12 <requirement type="package">perl-getopt-long-descriptive</requirement>
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13 </requirements>
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14 <command detect_errors="aggressive"><![CDATA[
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15 perl -Mlib='$__tool_directory__/lib' '$__tool_directory__/cpt_psm_2_gentable.pl'
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16 --galaxy
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17 --outfile_supporting '$__new_file_path__'
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18 --file "${file}"
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19
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20 #if $evalue and $evalue is not "None":
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21 --evalue "${evalue}"
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22 #end if
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23
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24 #if $dice and $dice is not "None":
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25 --dice "${dice}"
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26 #end if
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27
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28 #if $mismatch and $mismatch is not "None":
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29 --mismatch "${mismatch}"
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30 #end if
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31
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32 #if $gap_penalty and $gap_penalty is not "None":
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33 --gap_penalty "${gap_penalty}"
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34 #end if
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35
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36 #if $match and $match is not "None":
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37 --match "${match}"
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38 #end if
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39
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40 --diff_table "${diff_table}"
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41 --diff_table_files_path "${diff_table.files_path}"
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42 --diff_table_format TSV_U
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43 --diff_table_id "${diff_table.id}"
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44
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45 --blastclust "${blastclust}"
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46 --blastclust_files_path "${blastclust.files_path}"
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47 --blastclust_format TSV_U
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48 --blastclust_id "${blastclust.id}"
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49
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50 ]]></command>
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51 <inputs>
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52 <param name="file" help="PSM2 Data File" optional="False" label="file" type="data"/>
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53 <param value="0.0001" name="evalue" help="Evalue cutoff" optional="True" label="evalue" type="float"/>
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54 <param value="50" name="dice" help="Dice cutoff" optional="True" label="dice" type="float"/>
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55 <param value="-1" name="mismatch" help="Mismatch Score" optional="True" label="mismatch" type="float"/>
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56 <param value="0.0" name="gap_penalty" help="Gap Penalty" optional="True" label="gap_penalty" type="float"/>
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57 <param value="5" name="match" help="Match Score" optional="True" label="match" type="float"/>
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58 </inputs>
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59 <outputs>
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60 <data name="diff_table" format="tabular">
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61 </data>
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62 <data name="blastclust" format="tabular">
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63 </data>
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64 </outputs>
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65 <help>DESCRIPTION
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66 ===========
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67
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68 Following the execution of the PSM Prep tool, this tool simply aligns
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69 the genomes and generates a table comparison the positions of all
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70 proteins. It can be very useful to figure out which genes are missing in
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71 which genomes.
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72
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73 IMPORTANT PARAMETERS
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74 --------------------
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75
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76 - ``mismatch``, ``gap_penalty``, ``match``
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77
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78 These parameters control the Needleman-Wunsch Multiple Sequence
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79 Alignment library's scoring scheme. Mismatch scores are generally
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80 negative and discourage unrelated proteins from being plotted in a
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81 line together. Match scores encourage related proteins to line up.
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82 Gap penalty is set at zero as we generally prefer gaps to mismatches
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83 in this tool; phage genomes are small and gaps are "cheap" to use,
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84 whereas mismatches can sometimes give an incorrect impression of
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85 relatedness. That said, how your plots look is completely up to you
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86 and we encourage experimentation!
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87
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88
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89 </help>
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90 <tests/>
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91 </tool>