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annotate phykit_alignment_based.xml @ 0:37b049bf729a draft

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"planemo upload for repository https://github.com/JLSteenwyk/PhyKIT commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Mon, 28 Mar 2022 16:23:18 +0000
parents
children 1ac6ee298657
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1 <tool id="phykit_alignment_based" name="PhyKit - Alignment-based functions" version="0.1.0" python_template_version="3.5">
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2 <requirements>
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3 <requirement type="package" version="1.11.7">phykit</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6
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7 #if $tools.tool_selector == "create_concat"
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8 #import re
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9 touch 'aln_list.txt';
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10 #for $input in $tools.input1
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11 #set $safename = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
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12 ln -s '$input' $safename &&
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13 echo '$safename' >> 'aln_list.txt';
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14 #end for
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15 phykit create_concat -a 'aln_list.txt' -p 'out';
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16 cp out.fa ${fasta} ;
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17 cp out.partition ${partition} ;
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18 cp out.occupancy ${occupancy} ;
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19 #elif $tools.tool_selector == "pairwise_identity"
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20 phykit pairwise_identity $tools.input1 $tools.verbose > $pairwise_id;
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21 #elif $tools.tool_selector == "parsimony_informative_sites"
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22 phykit parsimony_informative_sites $tools.input1 > $parsimony_informative_sites;
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23 #end if
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24
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25 ]]></command>
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26 <inputs>
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27 <conditional name="tools">
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28 <param name="tool_selector" type="select" label="Select tool for processing the alignment(s)">
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29 <option value="create_concat">Concatenate alignments.</option>
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30 <option value="pairwise_identity">Calculate the average pairwise identity among sequences</option>
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31 <option value="parsimony_informative_sites">Calculate the number and percentage of parismony informative sites</option>
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32 </param>
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33 <when value="create_concat">
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34 <param name="input1" type="data" format="fasta" multiple="true" label="alignment list file. File should contain a single column list of alignment sequence files to concatenate into a single matrix." optional="false" />
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35 </when>
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36 <when value="pairwise_identity">
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37 <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" />
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38 <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False" label="optional argument to print all pairwise identities" />
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39 </when>
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40 <when value="parsimony_informative_sites">
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41 <param name="input1" type="data" format="fasta" multiple="false" label="Alignment file" optional="false" />
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data name="fasta" format="fasta" label="Concatenated fasta alignment file">
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47 <filter>tools['tool_selector']=='create_concat'</filter>
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48 </data>
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49 <data name="partition" format="iqtree" label="A partition file ready for input into RAxML or IQ-tree">
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50 <filter>tools['tool_selector']=='create_concat'</filter>
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51 </data>
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52 <data name="occupancy" format="txt" label="An occupancy file that summarizes the taxon occupancy per sequence">
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53 <filter>tools['tool_selector']=='create_concat'</filter>
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54 </data>
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55 <data name="pairwise_id" format="txt" label="Summary statistics unless used with the verbose option in which all pairwise identities will be reported.">
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56 <filter>tools['tool_selector']=='pairwise_identity'</filter>
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57 </data>
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58 <data name="parsimony_informative_sites" format="tabular" label="three tab delimited values: col1: number of parsimony informative sites col2: total number of sites col3: percentage of parsimony informative sites">
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59 <filter>tools['tool_selector']=='parsimony_informative_sites'</filter>
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60 </data>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="tool_selector" value="create_concat" />
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65 <param name="input1" value="12_YPR191W_Anc_7.548_codon_aln.fasta.clipkit,12_YPR190C_Anc_7.547_codon_aln.fasta.clipkit,12_YPR189W_Anc_7.546_codon_aln.fasta.clipkit"/>
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66 <output name="fasta" file="out.fa"/>
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67 <output name="partition" file="out.partition"/>
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68 <output name="occupancy" file="out.occupancy"/>
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69 </test>
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70 <test>
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71 <param name="tool_selector" value="pairwise_identity" />
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72 <param name="input1" value="test_alignment_0.fa"/>
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73 <param name="verbose" value="false" />
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74 <output name="pairwise_id" file="test_aln_pk_pi.txt"/>
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75 </test>
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76 <test>
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77 <param name="tool_selector" value="pairwise_identity" />
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78 <param name="input1" value="test_alignment_0.fa"/>
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79 <param name="verbose" value="true" />
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80 <output name="pairwise_id" file="test_aln_pk_pi_verbose.txt"/>
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81 </test>
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82 <test>
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83 <param name="tool_selector" value="parsimony_informative_sites" />
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84 <param name="input1" value="test_alignment_0.fa"/>
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85 <output name="parsimony_informative_sites" file="test_aln_pk_pis.txt"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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89
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90 Version: 1.11.3
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91 Citation: Steenwyk et al. 2021, Bioinformatics. doi: 10.1093/bioinformatics/btab096
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92 Documentation link: https://jlsteenwyk.com/PhyKIT/usage/index.html#alignment-based-functions
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93 Publication link: https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675
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94
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95 PhyKIT helps process and analyze multiple sequence alignments and phylogenies.
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96
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97 Generally, all functions are designed to help understand the contents of alignments
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98 (e.g., gc content or the number of parsimony informative sites) and the shape
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99 of trees (e.g., treeness, degree of violation of a molecular clock).
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100
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101
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102 Alignment-based commands
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103 ========================
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104 create_concatenation_matrix (alias: create_concat; cc)
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105 - create concatenation matrix from a set of alignments
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106 pairwise_identity (alias: pairwise_id, pi)
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107 - calculates average pairwise identify among sequences in
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108 an alignment file. This is a proxy for evolutionary rate
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109 parsimony_informative_sites (alias: pis)
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110 - calculates the number and percentage of parsimony
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111 informative sites in an alignment
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112
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113
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114 ]]></help>
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115 <citations>
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116 <citation type="bibtex">
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117 @misc{githubPhyKIT,
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118 author = {LastTODO, FirstTODO},
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119 year = {TODO},
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120 title = {PhyKIT},
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121 publisher = {GitHub},
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122 journal = {GitHub repository},
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123 url = {https://github.com/JLSteenwyk/PhyKIT},
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124 }</citation>
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125 </citations>
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126 </tool>