annotate enasearch_retrieve_data.xml @ 1:0719cfc3ebcb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/enasearch commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:08:14 -0500
parents cbc24be56f7b
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1 <tool id="enasearch_retrieve_data" name="Retrieve ENA data" version="@WRAPPER_VERSION@.0">
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2 <description>(other than taxon and project)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>search_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 enasearch
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11 retrieve_data
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12 @IDS@
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13 @DISPLAY@
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14 $expanded
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15 $header
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16 --file '$output'
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17 --download 'txt'
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18 ]]></command>
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19 <inputs>
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20 <param argument="--ids" type="text" multiple="true" label="Ids for records to return" help="Other than Taxon and Project. It can also be range of ids (e.g. ERA000010-ERA000020)"/>
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21 <expand macro="display_opt"/>
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22 <expand macro="expanded"/>
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23 <expand macro="header"/>
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="tabular" label="${tool.name} on ${ids}">
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27 <expand macro="change_format"/>
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="ids" value="ERA000010-ERA000020"/>
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33 <conditional name="display_opt">
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34 <param name="display" value="xml"/>
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35 </conditional>
1
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36 <output name="output" ftype="xml">
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37 <assert_contents>
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38 <has_text text="SUBMISSION accession=&quot;ERA000011&quot;" />
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39 <has_text text="SUBMISSION accession=&quot;ERA000012&quot;" />
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40 <has_text text="SUBMISSION accession=&quot;ERA000013&quot;" />
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41 <has_text text="SUBMISSION accession=&quot;ERA000014&quot;" />
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42 <has_text text="SUBMISSION accession=&quot;ERA000015&quot;" />
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43 <has_text text="SUBMISSION accession=&quot;ERA000016&quot;" />
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44 <has_text text="SUBMISSION accession=&quot;ERA000017&quot;" />
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45 <has_text text="SUBMISSION accession=&quot;ERA000018&quot;" />
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46 <has_text text="SUBMISSION accession=&quot;ERA000019&quot;" />
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47 <has_text text="SUBMISSION accession=&quot;ERA000020&quot;" />
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48 </assert_contents>
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49 </output>
0
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50 </test>
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51 <test>
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52 <param name="ids" value="A00145"/>
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53 <conditional name="display_opt">
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54 <param name="display" value="fasta"/>
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55 <param name="range_start" value="3"/>
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56 <param name="range_stop" value="63"/>
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57 </conditional>
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58 <output name="output" ftype="fasta" md5="758cb77161dcf6f8cf841cb141e9277e"/>
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59 </test>
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60 <test>
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61 <param name="ids" value="AL513382"/>
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62 <conditional name="display_opt">
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63 <param name="display" value="text"/>
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64 <param name="offset" value="0"/>
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65 <param name="length" value="100"/>
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66 </conditional>
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67 <param name="expanded" value="true"/>
1
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68 <output name="output" ftype="txt">
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69 <assert_contents>
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70 <has_text text="ID AL513382;" />
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71 </assert_contents>
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72 </output>
0
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73 </test>
1
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74 <!-- <test>
0
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75 <param name="ids" value="PRJEB2772,AL513382"/>
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76 <conditional name="display_opt">
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77 <param name="display" value="html"/>
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78 </conditional>
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79 <param name="header" value="true"/>
1
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80 <output name="output" ftype="html" md5="7b23a8c12893728272f4993073e341f6"/>
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81 </test> this seems broken at the moment -->
0
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82 </tests>
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83 <help><![CDATA[
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84 **What it does**
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85
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86 This tool retrieve ENA data (other than taxon and project)
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87 ]]></help>
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88 <expand macro="citations"/>
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89 </tool>