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kofamscan: remove entry from sample datatable (galaxyproject#5964)
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* kofamscan: remove entry from sample datatable

and switch default to tabular output

* profile + bump
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bernt-matthias authored Apr 25, 2024
1 parent 8f659e3 commit 431ba94
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Showing 2 changed files with 6 additions and 7 deletions.
10 changes: 5 additions & 5 deletions tools/kofamscan/kofamscan.xml
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@@ -1,8 +1,8 @@
<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<tool id="kofamscan" name="KofamScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
<description>gene function annotation based on KEGG orthology and HMM</description>
<macros>
<token name="@TOOL_VERSION@">1.3.0</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@VERSION_SUFFIX@">3</token>
<xml name="reportannotation" token_selected="">
<param name="reportannotation" type="boolean" truevalue="--report-unannotated" falsevalue="--no-report-unannotated" checked="@SELECTED@" label="Include sequence name to outputs even if no KOs are assigned?"/>
</xml>
Expand Down Expand Up @@ -95,8 +95,8 @@ $ap.f_cond.reportannotation
<param argument="-T" type="integer" value="1" label="Set threshold scale" help="The score thresholds will be multiplied by this value."/>
<conditional name="f_cond">
<param name="f_sel" type="select" label="Select output format">
<option value="detail" selected="true">Details for each hit (including hits below threshold) (detail)</option>
<option value="detail-tsv">Tab separeted values for detail format (detail-tsv)</option>
<option value="detail">Details for each hit (including hits below threshold) (detail)</option>
<option value="detail-tsv" selected="true">Tab separeted values for detail format (detail-tsv)</option>
<option value="mapper">KEGG Mapper compatible format (mapper)</option>
<option value="mapper-one-line">KEGG Mapper compatible format, but all hit KOs are listed in one line (mapper-oneline)</option>
</param>
Expand Down Expand Up @@ -333,4 +333,4 @@ More information are available on `GitHub <https://github.com/takaram/kofam_scan
<citations>
<citation type="doi">10.1093/bioinformatics/btz859</citation>
</citations>
</tool>
</tool>
3 changes: 1 addition & 2 deletions tools/kofamscan/tool-data/kofam_subset.loc.sample
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@@ -1,2 +1 @@
#value<tab>name<tab>kofam_value
subset.hal SUBSET test_value
#value<tab>name<tab>kofam_value

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