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annotate lasttrain.xml @ 5:f5a5a2b39ff2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 4568799de240022f4058ec1602e08f536916e2af"
author iuc
date Thu, 25 Mar 2021 20:53:27 +0000
parents 8705e0d74a0f
children 19c265784f35
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8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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1 <tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01">
0
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3 <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description>
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5 <macros>
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6 <import>macros_last.xml</import>
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7 </macros>
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9 <requirements>
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10 <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
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11 </requirements>
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9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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13 <command detect_errors="exit_code"><![CDATA[
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14 set -e -o pipefail;
0
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15 #if $db_opts.db_opts_input == 'lastdb'
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16 ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' &&
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17 #end if
4
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18 #if $query_fasta.ext.endswith('.gz')
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19 zcat
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20 #else
8705e0d74a0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 6b601baaf89634bc8d110ea06e3e64c7a585f3ba"
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21 cat
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22 #end if
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23 '$query_fasta' | last-train
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24
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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25 -Q $init_options.Q
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26 -r $init_options.r
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27 -q $init_options.q
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28 -a $init_options.cost_opt.a
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29 -b $init_options.cost_opt.b
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30 -A $init_options.cost_opt.A
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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31 -B $init_options.cost_opt.B
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32 -D $last_train_opt.align_opt.D
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33 #if $last_train_opt.align_opt.E != ""
3de2195f32c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
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34 -E $last_train_opt.align_opt.E
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35 #end if
0
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36 -s $last_train_opt.align_opt.s
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37 -S $last_train_opt.align_opt.S
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38 -T $last_train_opt.align_opt.T
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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39 -m $last_train_opt.align_opt.m
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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40 -k $last_train_opt.align_opt.k
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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41 -X $last_train_opt.align_opt.X
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42
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43 -P \${GALAXY_SLOTS:-1}
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44
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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45 #if $db_opts.db_opts_input == 'db'
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46 '${"' '".join(str($db_opts.database.fields.path).split(","))}'
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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47 #else if $db_opts.db_opts_input == 'lastdb'
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48 'db_files/lastdb'
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49 #end if
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50
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51 >'$outfile'
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52
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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53 ]]></command>
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54
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55 <inputs>
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56 <expand macro="input_db" />
4
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57 <param name="query_fasta" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Queries input files" />
0
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58 <conditional name="init_options">
1
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59 <param argument="-Q" type="select" multiple="false" label="Query input format">
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60 <option value="0" selected="true">FASTA</option>
0
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61 <option value="1">Fastq-sanger</option>
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62 </param>
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63 <when value="0">
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64 <param argument="-r" type="integer" value="5" label="Match score"/>
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65 <param argument="-q" type="integer" value="5" label="Mismatch cost"/>
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66 <expand macro="cost_macro" a="15" b="3"/>
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67 </when>
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68 <when value="1">
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69 <param argument="-r" type="integer" value="6" label="Match score"/>
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70 <param argument="-q" type="integer" value="18" label="Mismatch cost"/>
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71 <expand macro="cost_macro" a="21" b="9"/>
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72 </when>
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73 </conditional>
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74
9a7e91fc6562 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit c5689f5fc818d1538b2e15251c7de203c70e2219"
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75 <section name="last_train_opt" title="Last-train options" expanded="false">
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76 <!-- Training options missing -->
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77 <section name="align_opt" title="Alignment options" expanded="true">
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78 <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment"/>
3
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79 <param argument="-E" type="integer" value="" optional="true" label="Maximum expected alignments per square giga"/>
0
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80 <param argument="-s" type="select" multiple="false" label="Query strand to use">
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81 <option value="0">Reverse</option>
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82 <option value="1" selected="true">Forward</option>
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83 <option value="2">Both</option>
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84 </param>
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85 <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of:">
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86 <option value="0">Reference</option>
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87 <option value="1" selected="true">Query</option>
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88 </param>
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89 <!--<param name="gapless_align" argument="-C" type="integer" value="" label="Omit gapless alignments in COUNT others with > score-per-length"/>-->
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90 <param argument="-T" type="select" multiple="false" label="Type of alignment:">
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91 <option value="0" selected="true">Local</option>
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92 <option value="1">Overlap</option>
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93 </param>
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94 <param argument="-m" type="integer" value="10" label="Maximum initial matches per query position"/>
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95 <param argument="-k" type="integer" value="1" label="Use initial matches starting at every STEP-th position in each query"/>
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96 <param argument="-X" type="select" multiple="false" label="N/X is ambiguous in:">
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97 <option value="0" selected="true">Neither sequence</option>
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98 <option value="1">Reference</option>
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99 <option value="2">Query</option>
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100 <option value="3">Both</option>
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101 </param>
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102 </section>
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103 </section>
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104 </inputs>
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105
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106 <outputs>
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107 <data name="outfile" format="txt" label="LAST train from ${on_string}" />
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108 </outputs>
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109
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110 <tests>
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111 <test>
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112 <conditional name="db_opts">
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113 <param name="db_opts_input" value="db"/>
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114 <param name="database" value="humdb"/>
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115 </conditional>
3
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116 <section name="last_train_opt">
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117 <section name="align_opt">
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118 <param name="E" value="10"/>
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119 </section>
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120 </section>
4
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121 <param name="query_fasta" value="fuguMito.fa.gz" ftype="fasta.gz"/>
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122 <output name="outfile" file="last_train_E.txt" ftype="txt" lines_diff="28"/>
3
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123 </test>
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124 <test>
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125 <conditional name="db_opts">
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126 <param name="db_opts_input" value="db"/>
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127 <param name="database" value="humdb"/>
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128 </conditional>
4
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129 <param name="query_fasta" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/>
0
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130 <output name="outfile" file="last_train.txt" ftype="txt" lines_diff="22"/>
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131 </test>
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132 </tests>
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133
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134 <help>@LAST_HELP@</help>
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135 <citations><expand macro="citations"/></citations>
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136 </tool>