Mercurial > repos > iuc > cramino
changeset 2:8ea7960ef43c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino commit dc58f578ee856d4656a1f580cc2cf144f940797d
| author | iuc |
|---|---|
| date | Wed, 03 Dec 2025 16:06:43 +0000 |
| parents | ebf7acf24302 |
| children | |
| files | cramino.xml test-data/histcount.txt |
| diffstat | 2 files changed, 49 insertions(+), 13 deletions(-) [+] |
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--- a/cramino.xml Tue Oct 21 11:45:59 2025 +0000 +++ b/cramino.xml Wed Dec 03 16:06:43 2025 +0000 @@ -1,8 +1,8 @@ <tool id="cramino" name="Cramino" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> <description>Extract QC metrics from CRAM or BAM files</description> <macros> - <token name="@TOOL_VERSION@">1.1.0</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">cramino</requirement> @@ -35,13 +35,17 @@ --arrow $arrow_output #end if - #if $output_params.hist_out.hist.value == 'yes' - --hist $hist_output + #if $output_params.hist_out.histtype.value == 'hist' + --hist=$hist_output + $output_params.hist_out.scaled + #elif $output_params.hist_out.histtype.value == 'hist_count' + --hist-count=$hist_count_output $output_params.hist_out.scaled #end if - ##output capture - > $metrics + ## stdout output capture + > $metrics + ]]></command> <inputs> @@ -64,11 +68,15 @@ </param> <param argument="--arrow" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Write data to an arrow format file" help="An arrow file can be used with NanoPlot and NanoComp."/> <conditional name="hist_out"> - <param argument="--hist" type="select" label="Generate histograms" help="Histograms of read lengths and read identities."> - <option value="yes">Yes</option> + <param name="histtype" type="select" label="Generate histograms" help="Choose which histogram (data) to generate."> + <option value="hist">histogram (outputs actual histogram plot)</option> + <option value="hist_count">histogram counts (outputs read length histogram bin counts)</option> <option value="no" selected="true">No</option> </param> - <when value="yes"> + <when value="hist"> + <param argument="--scaled" type="boolean" checked="false" truevalue="--scaled" falsevalue="" label="Scale histogram" help="Scale histogram bins by total basepairs in each bin (not just read count)." /> + </when> + <when value="hist_count"> <param argument="--scaled" type="boolean" checked="false" truevalue="--scaled" falsevalue="" label="Scale histogram" help="Scale histogram bins by total basepairs in each bin (not just read count)." /> </when> <when value="no"/> @@ -81,7 +89,10 @@ <filter>output_params['arrow'] is True</filter> </data> <data name="hist_output" format="txt" label="${tool.name} on ${input_file.name}: Histogram Output"> - <filter>output_params['hist_out']['hist'] == "yes"</filter> + <filter>output_params['hist_out']['histtype'] == "hist"</filter> + </data> + <data name="hist_count_output" format="txt" label="${tool.name} on ${input_file.name}: Histogram Counts"> + <filter>output_params['hist_out']['histtype'] == "hist_count"</filter> </data> </outputs> <tests> @@ -102,7 +113,7 @@ </section> <section name="output_params"> <conditional name="hist_out"> - <param name="hist" value="yes"/> + <param name="histtype" value="hist"/> </conditional> </section> <output name="metrics"> @@ -119,7 +130,7 @@ </section> <section name="output_params"> <conditional name="hist_out"> - <param name="hist" value="yes"/> + <param name="histtype" value="hist"/> </conditional> </section> <section name="output_params"> @@ -150,14 +161,32 @@ <has_text_matching expression=".num_reads.: 5"/> </assert_contents> </output> - + </test> + <test expect_num_outputs="2"> + <section name="inputs"> + <param name="input_file" value="basecalls.bam"/> + </section> + <section name="output_params"> + <conditional name="hist_out"> + <param name="histtype" value="hist_count"/> + </conditional> + </section> + <output name="metrics"> + <assert_contents> + <has_text text="File name"/> + <has_text text="Creation time"/> + </assert_contents> + </output> + <output name="hist_count_output" file="histcount.txt"/> </test> </tests> <help><![CDATA[ **Cramino - BAM/CRAM Inspector for Nanopore Data** + Cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing. It generates **summary statistics**, and assess **data quality**. + **Usage Instructions** 1. **Input File**: Upload a **BAM/CRAM file** as input.