Mercurial > repos > bgruening > gfastats
changeset 8:6ec1b853c8fd draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 53b8f235e87107323cc6e636cc0d069551a44dec
| author | bgruening |
|---|---|
| date | Thu, 10 Oct 2024 09:58:15 +0000 |
| parents | 3ef480892a9f |
| children | |
| files | gfastats.xml macros.xml test-data/dataset_01_a.fasta.gz test-data/test_01_a.fasta.gz |
| diffstat | 4 files changed, 22 insertions(+), 7 deletions(-) [+] |
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--- a/gfastats.xml Fri Dec 23 20:00:51 2022 +0000 +++ b/gfastats.xml Thu Oct 10 09:58:15 2024 +0000 @@ -1,10 +1,10 @@ -<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01"> - <description>the swiss army knife for genome assembly</description> +<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2"> + <description>The swiss army knife for Genome Assembly</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements" /> <expand macro="biotools"/> + <expand macro="requirements"/> <version_command>gfastats --version</version_command> <command detect_errors="exit_code"><![CDATA[ gfastats @@ -34,6 +34,7 @@ --homopolymer-compress $mode_condition.homopolymer_compress #end if $mode_condition.discover_paths + $mode_condition.remove_terminal_gaps -o dataset.$mode_condition.output_condition.out_format #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz'] #if $mode_condition.output_condition.line_length @@ -53,7 +54,7 @@ #else if $mode_condition.statistics_condition.selector == 'assembly' --nstar-report #else - --seq-report + --segment-report $mode_condition.statistics_condition.out_sequence #end if $mode_condition.locale @@ -146,6 +147,7 @@ <option value="largest">Largest</option> <option value="smallest">Smallest</option> </param> + <param argument="--remove-terminal-gaps" type="boolean" truevalue="--remove-terminal-gaps" falsevalue="" checked="false" label="Remove gaps from the beginning and end of sequences"/> <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." /> </when> <when value="statistics"> @@ -154,7 +156,7 @@ <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> <option value="size">Scaffold, contig or gap sizes (--out-size)</option> <option value="coordinates">AGP, contig or gap coordinates (--out-coord)</option> - <option value="sequence">Sequence statistics (--seq-report)</option> + <option value="sequence">Sequence statistics (--segment-report)</option> </param> <when value="size"> <param argument="--out-size" type="select" label="Feature for reporting sizes" @@ -228,6 +230,19 @@ </conditional> <output name="output" value="test_01.fasta.gz" ftype="fasta.gz"/> </test> + <!--Test 01 A) --> + <test expect_num_outputs="1"> + <param name="input_file" value="dataset_01.fastq.gz"/> + <conditional name="mode_condition"> + <param name="selector" value="manipulation"/> + <param name="swiss_army_knife" value="swiss_army.sak"/> + <param name="remove_terminal_gaps" value="true"/> + <conditional name="output_condition"> + <param name="out_format" value="fasta.gz"/> + </conditional> + </conditional> + <output name="output" value="test_01_a.fasta.gz" ftype="fasta.gz"/> + </test> <!--Test 02 --> <test expect_num_outputs="1"> <param name="input_file" value="dataset_01.fastq.gz"/> @@ -418,5 +433,5 @@ gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions. ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>