Mercurial > repos > abims-sbr > pogs

annotate POGs.xml @ 4:b7bd93fc0ac9 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 8a27e74e95c5639292ca09c7e1680acd1088dcdd-dirty
author abims-sbr
date Mon, 29 May 2017 07:45:07 -0400
parents be2128ad0030
children dad7053ba20e
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1 <tool name="POGs" id="POGs" version="1.0">
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3 <description>
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4 Find orthologous groups
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5 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <requirements>
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12 <expand macro="python_required" />
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13 </requirements>
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15 <command>
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16 <![CDATA[
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17 python $__tool_directory__/scripts/S01_get_locus_orthologs_part1_v2.py ${zip_file}
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18 > ${output} &&
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19
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20 python $__tool_directory__/scripts/S02_get_locus_orthologs_part2_v2.py ${zip} ${minseq} ${paralogs}
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21 >> ${output};
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22 ]]>
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23 </command>
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25 <inputs>
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26 <param name="zip" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file" help="Contains the files filter after the tool oase" />
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27 <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Choose your ZIP file " help="Contains homologous sequences in PROTEIC format, ONLY A ZIP FILE" />
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28 <param name="minseq" type="integer" value="3" label="Drop orthogroups with less than n species" />
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29 <param name="paralogs" type="select" label="Paralogs savage removal" help="Yes : orthogroups with paralogs will be fully removed. No : paralogs sequences will be (naively) filtered to keep only one sequence." >
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30 <option value="yes">Yes</option>
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31 <option value="no">No</option>
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32 </param>
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33 </inputs>
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35 <outputs>
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36 <data format="txt" name="output" label="POGs" />
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37 <data format="no_unzip.zip" name="output_zip" label="POGs_locus_orthologs_unaligned" from_work_dir="POGs_locus_orthologs_unaligned.zip" />
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38 </outputs>
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40 <tests>
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41 <test>
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42 <param name="zip" ftype="zip" value="outputfilter.zip" />
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43 <param name="zip_file" ftype="zip" value="outputpairwise.zip" />
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44 <param name="minseq" value="2" />
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45 <param name="paralogs" value="no" />
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46 <output name="output" value="test_03.out" />
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47 </test>
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48 <test>
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49 <param name="zip" ftype="zip" value="outputfilter.zip" />
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50 <param name="zip_file" ftype="zip" value="outputpairwise.zip" />
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51 <param name="minseq" value="2" />
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52 <param name="paralogs" value="yes" />
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53 <output name="output" value="test_03b.out" />
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54 </test>
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55 </tests>
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57 <help>
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58 ============
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59 What it does
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60 ============
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62 | This tool takes a zip archive containing nucleic fasta sequence files and a zip archive containing a file per pairwise with the homologous sequences (in proteic format). It searches for orthologous sequences.
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63 | There are 2 outputs.
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64 |
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65 | The script was written by **Eric Fontanillas**.
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66 | The wrapper was written by **Julie Baffard**.
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67 | Last improvments (paralogous filtering and code factoring) made by Victor Mataigne.
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70 --------
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72 ======
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73 Inputs
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74 ======
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76 option **Select a zip file containing the input files** :
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78 | the input zip file must have the extension .ort.zip
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79 | At the beginning, when you upload your input, you have to change the extension .zip to .ort.zip
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82 --------
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84 =======
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85 Outputs
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86 =======
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88 This tool, produces the following files :
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90 **POGs** :
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92 | is the general output. It gives different informations : number of locus, each locus, ...
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93 | it gives for example, all the locus containing 2 species :
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94 | 2_sp : [[name_of_sequence,name_of_squence],...,[name_of_sequence, name_of_sequence]]
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95 | it's the same for locus containing 3 species, 4 species, ...
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96 |
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97
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98 **POGs_locus_orthologs_unaligned** :
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99
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100 | is the output (in zip format) which contains each locus.
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101 | one file corresponding to one locus.
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102
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103 the sequences of each locus are in nucleic format.
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104
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105 .. class:: warningmark
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106
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107 The zip output has to be downloaded (and extracts the files with a file archiver software), you cannot visualize them with the "eye icon" through the interface.
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108
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109 </help>
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110
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111 <expand macro="citations" />
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112
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113 </tool>