Mercurial > repos > gga > askomics_integrate

annotate askomics.xml @ 0:d2aeb7a02bb2 draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics commit f745b23c84a615bf434d717c8c0e553a012f0268
author gga
date Mon, 11 Sep 2017 05:48:41 -0400
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d2aeb7a02bb2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
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2 <tool id="askomics_integrate" name="AskOmics" version="@WRAPPER_VERSION@">
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3 <description>Data integration</description>
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4
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8
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9 <expand macro='requirements' />
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10
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11 <stdio>
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12 <exit_code range="1:" />
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13 </stdio>
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d2aeb7a02bb2 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/askomics commit f745b23c84a615bf434d717c8c0e553a012f0268
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15 <command><![CDATA[
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16 askocli integrate
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18 #if @URL@
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19 -a @URL@
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20 #else
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21 -a @ENV_URL@
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22 #end if
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24 --file-type '$input_format.format'
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26 #if $input_format.format == "csv"
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27
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28 #if $input_format.opt.headers
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29 --headers $input_format.opt.headers
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30 #end if
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31
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32 #if $input_format.opt.col_type
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33 -c $input_format.opt.col_type
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34 #end if
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35
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36 #if $input_format.opt.key_col
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37 --key-columns $input_format.opt.key_col
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38 #end if
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39
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40 #if $input_format.opt.dis_col
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41 --disabled-columns $input_format.opt.dis_col
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42 #end if
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43
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44 #end if
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46 #if $input_format.format == "gff"
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47 -e $input_format.ent
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48 -t '$input_format.tax'
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49 #end if
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50
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51 #if $input_format.format == "bed"
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52 --entity-name $input_format.ent_name
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53 -t '$input_format.tax'
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54 #end if
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55
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56 #if $advanced.uri
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57 --uri $advanced.uri
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58 #end if
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59
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60 $advanced.public
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61
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62 -k @APIKEY@
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63
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64 '$input'
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65 > '$output'
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66 ]]></command>
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67
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68 <inputs>
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69 <expand macro='askomics_loc' />
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70 <expand macro='askomics_auth' />
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71
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72 <conditional name="input_format">
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73 <param type="select" name="format" label="Input format">
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74 <option value="csv">CSV/TSV</option>
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75 <option value="gff">GFF</option>
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76 <option value="ttl">Turtle</option>
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77 <option value="bed">BED</option>
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78 </param>
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79 <when value="csv">
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80 <param format="tabular" name="input" type="data" label="Dataset to integrate" />
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81 <section name='opt' title='Optional fields' expanded='false'>
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82 <param name="headers" type="text" value="" optional="true" label="Headers (separated with spaces)" argument="--headers" />
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83 <param name="col_type" type="text" value="" optional="true" label="Columns types (separated with spaces)" argument="-c" />
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84 <param name="key_col" type="text" value="" optional="true" label="Key columns (separated with spaces)" argument="--key-columns" />
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85 <param name="dis_col" type="text" value="" optional="true" label="Disabled columns (separated with spaces)" argument="--disabled-columns" />
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86 </section>
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87 </when>
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88 <when value="gff">
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89 <param format="gff3" name="input" type="data" label="Dataset to integrate" />
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90 <param name="ent" type="text" value="transcript gene" label="Entities (separated with space)" argument="-e" />
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91 <param name="tax" type="text" value="" label="Taxon" argument="-t" />
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92 </when>
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93 <when value="bed">
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94 <param format="bed" name="input" type="data" label="Dataset to integrate" />
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95 <param name="ent_name" type="text" value="" label="Entity name" argument="--entity-name" />
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96 <param name="tax" type="text" value="" label="Taxon" argument="-t" />
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97 </when>
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98 <when value="ttl">
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99 <param format="ttl" name="input" type="data" label="Dataset to integrate" />
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100 </when>
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101 </conditional>
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102
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103 <!-- Advanced fonctionalities -->
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104 <section name="advanced" title="Advanced features" expanded="false">
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105 <param name="uri" type="text" value="" label="Custom URI" argument="--uri" />
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106 <param name="public" type="boolean" checked="false" truevalue="--public" falsevalue="" label="Integrate as a public dataset" argument="--public" />
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107 </section>
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108
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109 </inputs>
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110
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111 <outputs>
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112 <data format="txt" name="output" label="Integration of ${input_format.input.name}" />
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113 </outputs>
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114
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115 <tests>
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116 <test expect_failure='true' expect_exit_code='1'>
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117 <expand macro='test_asko_loc' />
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118 <expand macro='test_asko_auth' />
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119 <conditional name='input_format'>
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120 <param name='format' value='csv' />
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121 <param name='input' value='people.tsv' />
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122 </conditional>
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123 </test>
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124 </tests>
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125
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126 <help><![CDATA[
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127 @HELP@
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128 ]]></help>
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129
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130 <expand macro='citation' />
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131 </tool>