Mercurial > repos > youyuh48 > centrifuge_kreport

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author youyuh48
date Tue, 05 Feb 2019 03:08:48 -0500
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1 <tool id="centrifuge_kreport" name="centrifuge_kreport" version="0.1.0">
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2 <description>Centrifuge-kreport creates Kraken-style reports from centrifuge out files</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.3">centrifuge</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8 centrifuge-kreport
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9 -x '${db.fields.path}'
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11 #if $settings.advanced == "advanced"
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12 $settings.only_unique
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13 $settings.show_zeros
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14 $settings.count_table
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15 --min-score $settings.min_score
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16 --min-length $settings.min_length
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17 #end if
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18
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19 $input > output.txt
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param type="data" name="input" format="tabular"/>
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24 <param name="db" type="select" label="Select a reference database">
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25 <options from_data_table="centrifuge_indices">
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26 <filter type="sort_by" column="2"/>
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27 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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28 </options>
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29 </param>
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30 <conditional name="settings">
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31 <param name="advanced" type="select" label="Specify advanced parameters">
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32 <option value="simple" selected="true">No, use program defaults.</option>
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33 <option value="advanced">Yes, see full parameter list.</option>
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34 </param>
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35 <when value="simple"></when>
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36 <when value="advanced">
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37 <param name="only_unique" type="boolean" truevalue="--only-unique" falsevalue="" checked="false" label="Only count reads that were uniquely assigned to one taxon"/>
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38 <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="false" label="Show clades that have zero reads, too"/>
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39 <param name="count_table" type="boolean" truevalue="--is-count-table" falsevalue="" label="The format of the file is 'TAXID-tab-COUNT' instead of the standard Centrifuge output format"/>
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40 <param name="min_score" type="integer" label="--min-score" value="0" min="0" help="Require a minimum score for reads to be counted"/>
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41 <param name="min_length" type="integer" label="--min-length" value="0" min="0" help="Require a minimum alignment length to the read"/>
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42 </when>
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43 </conditional>
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44 </inputs>
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45 <outputs>
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46 <data format="tabular" name="output" from_work_dir="output.txt" label="${tool.name} on ${on_string}"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input" value="test-data_centrifuge-kreport/defaults.tsv"/>
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51 <output name="output" file="defaults.tsv.kreport"/>
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52 </test>
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53 </tests>
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54 <help>
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55 <![CDATA[
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56 centrifuge-kreport creates Kraken-style reports from centrifuge out files.
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57 ]]>
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58 </help>
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59 <citations>
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60 <citation type="doi">10.1101/gr.210641.116</citation>
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61 </citations>
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62 </tool>