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planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
author sanbi-uwc
date Tue, 19 Jul 2022 11:57:59 +0000
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f2a7aaf93a1d planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty
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1 <tool id="summarize_poliovirus_alignment" name="Summarize poliovirus alignment" version="0.1.0+galaxy1" profile="21.05">
0
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2 <requirements>
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3 <requirement type="package" version="3.9">python</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 python $__tool_directory__/summarize_alignment.py
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7 --summary_output_filename '$output1'
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8 --variant_list_outputs
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9 #for $key in $variant_list.keys()
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10 '$variant_list[$key]'
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11 #end for
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12 --datasets
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13 #for $dataset in $alignment_assessments
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14 '$dataset'
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15 #end for
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16
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17 ]]></command>
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18 <inputs>
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19 <!-- input is list of reports for poliovirus sabin 1, 2 and 3 -->
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20 <param name="alignment_assessments" format="json" type="data_collection" collection_type="list" label="Poliovius alignment assessments" help="Input is a list of JSON reports from the assess_poliovirus_alignment tool" />
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21 </inputs>
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22 <outputs>
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23 <data name="output1" format="tabular" label="Poliovirus variant summary on ${on_string}" />
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24 <collection name="variant_list" type="list" label="Poliovirus variant lists on ${on_string}" structured_like="alignment_assessments" format="tabular">
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25 <!-- todo - find a way to set the metadata columns for the tabular datasets -->
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26 </collection>
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27 </outputs>
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28 <tests>
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29 <test expect_num_outputs="3">
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30 <param name="alignment_assessments" ftype="json">
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31 <collection type="list">
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32 <element name="sample1" value="sample1_output.json" />
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33 </collection>
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34 </param>
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35 <output name="output1" ftype="tabular">
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36 <assert_contents>
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37 <has_text text="23:G:A;26:G:A;38:A:G;40:T:C;59:C:T;65:T:C;72:A:G;" />
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38 </assert_contents>
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39 </output>
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40 <output_collection name="variant_list">
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41 <element name="sample1" file="sample1_variants.tabular" ftype="tabular" />
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42 </output_collection>
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 Given a list of outputs of the assess_poliovirus_alignment tool, make a final summary.
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47 ]]></help>
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48 <citations>
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49 <citation type="bibtex"><![CDATA[
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50 @software{van_Heusden_Poliovirus_variation_reporting_2022,
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51 author = {van Heusden, Peter},
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52 month = {7},
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53 title = {{Poliovirus variation reporting scripts}},
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54 url = {https://github.com/pvanheus/polio_report},
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55 version = {0.1.0},
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56 year = {2022}
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57 }
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58 ]]></citation>
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59 </citations>
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60 </tool>