| Previous changeset 23:e2bbc79f0fac (2023-01-25) Next changeset 25:74babe57d739 (2023-01-27) |
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Commit message:
"planemo upload commit a0a9b02c60a91942a271b8b35648c0b152fe1ebd-dirty" |
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modified:
dante.xml dante_gff_output_filtering.xml dante_gff_to_dna.xml dante_gff_to_tabular.xml summarize_gff.xml |
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| diff -r e2bbc79f0fac -r df99812ded92 dante.xml --- a/dante.xml Wed Jan 25 13:06:55 2023 +0000 +++ b/dante.xml Fri Jan 27 08:15:31 2023 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.4"> +<tool id="dante" name="Domain based ANnotation of Transposable Elements - DANTE" version="1.1.5"> <description> Tool for annotation of transposable elements based on the similarity to conserved protein domains database. </description> <requirements> - <requirement type="package">dante=0.1.4</requirement> + <requirement type="package">dante=0.1.5</requirement> </requirements> <stdio> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> @@ -17,12 +17,10 @@ #end if && - dante --query \${INPUT_SEQUENCES} --domain_gff ${DomGff} --database $database --scoring_matrix ${scoring_matrix} - - && + --cpu \${GALAXY_SLOTS:-1} dante_gff_output_filtering.py --dom_gff ${DomGff} --domains_prot_seq ${Domains_filtered} --domains_filtered ${DomGff_filtered} --output_dir . |
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| diff -r e2bbc79f0fac -r df99812ded92 dante_gff_output_filtering.xml --- a/dante_gff_output_filtering.xml Wed Jan 25 13:06:55 2023 +0000 +++ b/dante_gff_output_filtering.xml Fri Jan 27 08:15:31 2023 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="domains_filter" name="Protein Domains Filter" version="1.1.4"> +<tool id="domains_filter" name="Protein Domains Filter" version="1.1.5"> <description> Tool for filtering of gff3 output from DANTE. Filtering can be performed based domain type and alignment quality. </description> <requirements> - <requirement type="package">dante=0.1.4</requirement> + <requirement type="package">dante=0.1.5</requirement> </requirements> <stdio> <regex match="Traceback" source="stderr" level="fatal" description="Unknown error" /> |
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| diff -r e2bbc79f0fac -r df99812ded92 dante_gff_to_dna.xml --- a/dante_gff_to_dna.xml Wed Jan 25 13:06:55 2023 +0000 +++ b/dante_gff_to_dna.xml Fri Jan 27 08:15:31 2023 +0000 |
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| @@ -1,7 +1,7 @@ -<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.4"> +<tool id="domains_extract" name="Extract Domains Nucleotide Sequences" version="1.1.5"> <description> Tool to extract nucleotide sequences of protein domains found by DANTE </description> <requirements> - <requirement type="package">dante=0.1.4</requirement> + <requirement type="package">dante=0.1.5</requirement> </requirements> <command> TEMP_DIR_LINEAGES=\$(mktemp -d) && |
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| diff -r e2bbc79f0fac -r df99812ded92 dante_gff_to_tabular.xml --- a/dante_gff_to_tabular.xml Wed Jan 25 13:06:55 2023 +0000 +++ b/dante_gff_to_tabular.xml Fri Jan 27 08:15:31 2023 +0000 |
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| @@ -1,6 +1,6 @@ -<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="0.1.4" python_template_version="3.5"> +<tool id="gff_to_tabular" name="Convert dante gff3 to tab delimited file" version="0.1.5" python_template_version="3.5"> <requirements> - <requirement type="package">dante=0.1.4</requirement> + <requirement type="package">dante=0.1.5</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ summarize_gff.R '$inputgff' '$output' |
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| diff -r e2bbc79f0fac -r df99812ded92 summarize_gff.xml --- a/summarize_gff.xml Wed Jan 25 13:06:55 2023 +0000 +++ b/summarize_gff.xml Fri Jan 27 08:15:31 2023 +0000 |
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| @@ -1,6 +1,6 @@ -<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="0.1.4" python_template_version="3.5"> +<tool id="gff_summary" name="Summarize gff3 output from DANTE" version="0.1.5" python_template_version="3.5"> <requirements> - <requirement type="package">dante=0.1.4</requirement> + <requirement type="package">dante=0.1.5</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ summarize_gff.R '$inputgff' '$output' '$group' |