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annotate macros.xml @ 3:236155b4e5f9 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
author gga
date Wed, 20 Sep 2017 09:43:36 -0400
parents b4a85d0c85b8
children 5559e41721c3
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="2.7">python</requirement>
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6 <requirement type="package" version="1.65">biopython</requirement>
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7 <requirement type="package" version="0.6.2">bcbiogff</requirement>
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8 <requirement type="package" version="2.12.4">requests</requirement>
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9 <requirement type="package" version="0.16.0">future</requirement>
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10 <yield/>
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11 </requirements>
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12 </xml>
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13 <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
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14 <token name="@EXT_URL@">
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15 "\$GALAXY_WEBAPOLLO_EXT_URL"
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16 </token>
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17 <token name="@URL@">
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18 "\$GALAXY_WEBAPOLLO_URL"
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19 </token>
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20 <token name="@ADMIN_AUTH@">
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21 "\$GALAXY_WEBAPOLLO_URL"
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22 "\$GALAXY_WEBAPOLLO_USER"
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23 "\$GALAXY_WEBAPOLLO_PASSWORD"
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24 </token>
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25
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26 <token name="@ORG_OR_GUESS@">
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27 <![CDATA[
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28 #if $org_source.source_select == "auto_json":
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29 --org_json "${org_source.org_file}"
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30 #elif $org_source.source_select == "select":
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31 --org_id "${org_source.org_select}"
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32 #else:
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33 --org_raw "${org_source.org_raw}"
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34 #end if
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35 ]]>
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36 </token>
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37 <token name="@ORG_CN_OR_GUESS@">
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38 <![CDATA[
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39 @ORG_OR_GUESS@
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40
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41 #if $cn_source.source_select == "auto":
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42 #if str($cn_source.cn_file) != "None":
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43 --seq_fasta $cn_source.cn_file
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44 #end if
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45 #else
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46 #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
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47 --seq_raw
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48 #for $item in $cn_source.refseqs:
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49 "${item.refseq}"
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50 #end for
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51 #end if
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52 #end if
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53 ]]>
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54 </token>
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55 <xml name="org_or_guess">
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56 <conditional name="org_source">
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57 <param name="source_select" type="select" label="Organism Common Name Source">
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58 <option value="select">Select</option>
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59 <option value="direct">Direct Entry</option>
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60 <option value="auto_json">Autodetect from Apollo JSON</option>
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61 </param>
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62 <when value="select">
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63 <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
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64 </when>
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65 <when value="direct">
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66 <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
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67 </when>
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68 <when value="auto_json">
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69 <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
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70 </when>
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71 </conditional>
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72 </xml>
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73 <xml name="cn_or_guess">
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74 <expand macro="org_or_guess" />
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75 <conditional name="cn_source">
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76 <param name="source_select" type="select" label="Organism Sequence(s) Source">
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77 <option value="all">All Refseqs</option>
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78 <option value="direct">Direct Entry</option>
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79 <option value="auto">Autodetect from Fasta</option>
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80 </param>
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81 <when value="all">
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82 </when>
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83 <when value="auto">
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84 <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
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85 </when>
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86 <when value="direct">
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87 <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
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88 <param name="refseq" type="text" label="Reference sequence(s)" />
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89 </repeat>
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90 </when>
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91 </conditional>
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92 </xml>
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93
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94 <xml name="test_result">
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95 <assert_stderr>
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96 <has_text text="MissingSchema" />
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97 </assert_stderr>
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98 </xml>
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99
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100 <xml name="citations">
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101 <citations>
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102 </citations>
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103 </xml>
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104 <xml name="gff3_input">
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105 <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
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106 </xml>
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107 <token name="@GENOME_SELECTOR_PRE@">
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108 #if $reference_genome.reference_genome_source == 'history':
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109 ln -s $reference_genome.genome_fasta genomeref.fa;
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110 #end if
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111 </token>
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112 <token name="@GENOME_SELECTOR@">
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113 #if $reference_genome.reference_genome_source == 'cached':
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114 "${reference_genome.fasta_indexes.fields.path}"
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115 #elif $reference_genome.reference_genome_source == 'history':
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116 genomeref.fa
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117 #end if
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118 </token>
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119 <token name="@REFERENCES@">
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120 <![CDATA[
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121 ------
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122
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123 **Citation**
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124
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125 If you use this tool in Galaxy, please cite:
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126 Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
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127 ]]>
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128 </token>
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129 </macros>