Mercurial > repos > petr-novak > dante_ltr
changeset 17:d1c3b29b1478 draft
planemo upload commit ce025ba66edc87ff8ced32d5fdb36109f12cebf0-dirty
author | petr-novak |
---|---|
date | Thu, 10 Aug 2023 12:22:28 +0000 |
parents | 7ec262f92d89 |
children | 05551747b2c3 |
files | clean_dante_ltr.xml dante_ltr_search.xml dante_ltr_summary.xml dante_ltr_to_library.xml macros.xml |
diffstat | 5 files changed, 54 insertions(+), 14 deletions(-) [+] |
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--- a/clean_dante_ltr.xml Wed May 10 13:07:41 2023 +0000 +++ b/clean_dante_ltr.xml Thu Aug 10 12:22:28 2023 +0000 @@ -1,7 +1,8 @@ -<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="0.2.2.4" python_template_version="3.5"> - <requirements> - <requirement type="package" version="0.2.2.4">dante_ltr</requirement> - </requirements> +<tool id="clean_dante_ltr" name="DANTE_LTR retrotransposons filtering" version="@TOOL_VERSION@" python_template_version="3.5"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ clean_ltr.R --gff3 '$dante_ltr' --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} &&
--- a/dante_ltr_search.xml Wed May 10 13:07:41 2023 +0000 +++ b/dante_ltr_search.xml Thu Aug 10 12:22:28 2023 +0000 @@ -1,7 +1,8 @@ -<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="0.2.2.4" python_template_version="3.5"> - <requirements> - <requirement type="package" version="0.2.2.4">dante_ltr</requirement> - </requirements> +<tool id="dante_ltr_search" name="DANTE_LTR retrotransposon identification" version="@TOOL_VERSION@" python_template_version="3.5"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ echo \$PATH &&
--- a/dante_ltr_summary.xml Wed May 10 13:07:41 2023 +0000 +++ b/dante_ltr_summary.xml Thu Aug 10 12:22:28 2023 +0000 @@ -1,9 +1,10 @@ -<tool id="dante_ltr_summary" name="Summarize DANTE_LTR output" version="0.2.2.4" python_template_version="3.5"> - <requirements> - <requirement type="package" version="0.2.2.4">dante_ltr</requirement> - </requirements> +<tool id="dante_ltr_summary" name="Summarize DANTE_LTR output" version="@TOOL_VERSION@" python_template_version="3.5"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ - dante_ltr_summary.R -g '$input1' -o output && + dante_ltr_summary -g '$input1' -o output && mv output.pdf '$output1' ]]></command> <inputs> @@ -15,4 +16,4 @@ <help><![CDATA[ This tool takes GFF3 output from DANTE_LTR and make graphical summary of the results. ]]></help> -</tool> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dante_ltr_to_library.xml Thu Aug 10 12:22:28 2023 +0000 @@ -0,0 +1,28 @@ +<tool id="dante_ltr_to_library" name="Create representative library from DANTE_LTR output " version="@TOOL_VERSION@" python_template_version="3.5"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + cp '$dante_ltr' dante_ltr.gff3 && + dante_ltr_to_library --gff3 dante_ltr.gff3 --reference_sequence '$reference' --output output --cpu \${GALAXY_SLOTS:-1} --min_coverage 3 + && + ls -l output + && + mv output/mmseqs2/mmseqs_representative_seq_clean.fasta $dante_ltr_library + ]]></command> + <inputs> + <param type="data" name="dante_ltr" format="gff3" + label="GFF3 output from DANTE_LTR retrotransposon identification pipeline"/> + <param type="data" name="reference" format="fasta" label="Reference sequence matching input GFF3" /> + </inputs> + <outputs> + <data name="dante_ltr_library" format="fasta" + label="Representative library from DANTE_LTR $dante_ltr.hid on reference $reference.hid"/> + </outputs> + <help><![CDATA[ + This tool extract representative sequences from LTR-RT library identified + by DANTE_LTR. Resulting library is suitable for RepeatMasker search. + ]]></help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Aug 10 12:22:28 2023 +0000 @@ -0,0 +1,9 @@ +<macros> + <token name="@TOOL_VERSION@">2.3.3</token> + <token name="@REQUIREMENT_VERSION@">0.2.3.3</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@REQUIREMENT_VERSION@">dante_ltr</requirement> + </requirements> + </xml> +</macros> \ No newline at end of file