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"planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
author nml
date Tue, 23 Jun 2020 10:25:53 -0400
parents 89c3ba37711c
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2fbea749a1d1 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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1 <tool id="filterstat" name="Filter Stats" version ="@VERSION@+galaxy1">
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2 <description>Identify number of positions excluded based on filtered status</description>
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3 <macros>
2fbea749a1d1 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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4 <import>macros.xml</import>
2fbea749a1d1 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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5 </macros>
2fbea749a1d1 "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 57067916cb7b9c5b65c1da59d4bbb846c3e3af2f"
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code">
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8 filter-stats.pl -i $tabfile
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9 #if $summary:
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10 -a
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11 #end if
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12 > $out
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13 </command>
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14 <inputs>
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15 <param name="tabfile" type="data" label="SNV-alignment positions tab delimited file" format="tabular"/>
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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16 <param name="summary" type="select" display="checkboxes" label="Summary Options" multiple="true">
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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17 <option value="invalids">Include all entries marked as 'filtered-invalid'</option>
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18 </param>
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" name="out" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="tabfile" value="filter-stats-in.tsv" />
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26 <output name="out" file="filter-stats-out.tabular" />
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27 </test>
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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28 </tests>
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89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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30 <help>
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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31 What it does
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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32 ============
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33
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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34 This script prints a stat summary of the number of N's and -'s found in the SNV-alignment positions tab delimited file.
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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37 Usage
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38 =====
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39
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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40 **Parameters**
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41 - input - The SNV-alignment positions tab delimited file
89c3ba37711c "planemo upload for repository https://github.com/phac-nml/snvphyl-galaxy commit 90a172f1fc12b9c4d73f4c924a8c0c5a559589d0"
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43
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44 **Options**
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45 - -all When this option is set, the summary will include all the entries marked as 'filtered-invalid'
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46 </help>
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47 <expand macro="citations"/>
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48 </tool>