| Previous changeset 2:be6bbdeafcb8 (2021-10-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 412a084cda6aeca8dfe0b0dbfff9c3426aec7707 |
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modified:
metaeuk_easy_predict.xml test-data/output.gff |
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| diff -r be6bbdeafcb8 -r 860f8836c936 metaeuk_easy_predict.xml --- a/metaeuk_easy_predict.xml Thu Oct 21 16:10:35 2021 +0000 +++ b/metaeuk_easy_predict.xml Fri Oct 04 08:57:34 2024 +0000 |
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| @@ -1,11 +1,11 @@ -<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0"> +<tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy1" profile="23.0"> <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description> + <macros> + <token name="@TOOL_VERSION@">7.bba0d80</token> + </macros> <xrefs> <xref type="bio.tools">MetaEuk</xref> </xrefs> - <macros> - <token name="@TOOL_VERSION@">5.34c21f2</token> - </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> </requirements> @@ -16,7 +16,7 @@ '$query' output.fasta "./tmp/metaeuk_working" - --threads \${GALAXY_SLOTS:-1} + --threads "\${GALAXY_SLOTS:-1}" --min-length '${min_length}' -e '${segment_eval}' --metaeuk-eval '${metaeuk_eval}' @@ -33,17 +33,17 @@ <param name="contigs" type="data" format="fasta" label="Contigs to search again" /> <param name="query" type="data" format="fasta" label="Proteins to search against contigs" /> <param argument="-e" name="segment_eval" type="float" value="100" label="Maximum e-value of individual match segment" /> - <param argument="--min-length" name="min_length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" /> - <param argument="--metaeuk-eval" name="metaeuk_eval" type="float" value="0.001" label="Maximum e-value of combined exon set" /> - <param argument="--metaeuk-tcov" name="metaeuk_tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" /> + <param argument="--min-length" type="integer" value="15" label="Minimum number of codons in predicted open reading frame" /> + <param argument="--metaeuk-eval" type="float" value="0.001" label="Maximum e-value of combined exon set" /> + <param argument="--metaeuk-tcov" type="float" value="0.5" label="Minimum length ratio of combined exon set to target" /> <conditional name="adv"> <param type="select" name="adv_options" label="Show advanced options"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> - <param argument="--max-intron" name="max_intron" value="10000" type="integer" label="Maximum intron size" /> - <param argument="--min-intron" name="min_intron" value="15" type="integer" label="Minimum intron size" /> + <param argument="--max-intron" value="10000" type="integer" label="Maximum intron size" /> + <param argument="--min-intron" value="15" type="integer" label="Minimum intron size" /> </when> <when value="no"> </when> @@ -54,8 +54,8 @@ </param> </inputs> <outputs> - <data name="output" format="fasta" /> - <data name="gff_output" format="gff" /> + <data name="output" format="fasta" label="${tool.name} on ${on_string}: FASTA" /> + <data name="gff_output" format="gff" label="${tool.name} on ${on_string}: GFF" /> </outputs> <tests> |
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| diff -r be6bbdeafcb8 -r 860f8836c936 test-data/output.gff --- a/test-data/output.gff Thu Oct 21 16:10:35 2021 +0000 +++ b/test-data/output.gff Fri Oct 04 08:57:34 2024 +0000 |
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| @@ -1,14 +1,14 @@ -my_multi_exon_contig_1 gene MetaEuk 101 1142 629 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+ -my_multi_exon_contig_1 mRNA MetaEuk 101 1142 629 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA;Parent=identical_all_3_exons|my_multi_exon_contig_1|+ -my_multi_exon_contig_1 exon MetaEuk 101 430 235 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA -my_multi_exon_contig_1 CDS MetaEuk 101 430 235 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon -my_multi_exon_contig_1 exon MetaEuk 481 882 272 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA -my_multi_exon_contig_1 CDS MetaEuk 481 882 272 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon -my_multi_exon_contig_1 exon MetaEuk 945 1142 128 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_exon;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_mRNA -my_multi_exon_contig_1 CDS MetaEuk 969 1142 128 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+_CDS;Parent=identical_all_3_exons|my_multi_exon_contig_1|+_exon -my_multi_exon_contig_2 gene MetaEuk 101 723 402 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+ -my_multi_exon_contig_2 mRNA MetaEuk 101 723 402 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA;Parent=identical_all_2_exons|my_multi_exon_contig_2|+ -my_multi_exon_contig_2 exon MetaEuk 101 430 235 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_exon;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA -my_multi_exon_contig_2 CDS MetaEuk 101 430 235 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_CDS;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_exon -my_multi_exon_contig_2 exon MetaEuk 481 723 166 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_exon;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_mRNA -my_multi_exon_contig_2 CDS MetaEuk 481 723 166 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+_CDS;Parent=identical_all_2_exons|my_multi_exon_contig_2|+_exon +my_multi_exon_contig_1 MetaEuk gene 101 1142 629 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100 +my_multi_exon_contig_1 MetaEuk mRNA 101 1142 629 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100 +my_multi_exon_contig_1 MetaEuk exon 101 430 235 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_0;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA +my_multi_exon_contig_1 MetaEuk CDS 101 430 235 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_0;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_0 +my_multi_exon_contig_1 MetaEuk exon 481 882 272 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_1;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA +my_multi_exon_contig_1 MetaEuk CDS 481 882 272 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_1;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_1 +my_multi_exon_contig_1 MetaEuk exon 945 1142 128 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_2;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_mRNA +my_multi_exon_contig_1 MetaEuk CDS 969 1142 128 + . Target_ID=identical_all_3_exons;TCS_ID=identical_all_3_exons|my_multi_exon_contig_1|+|100_CDS_2;Parent=identical_all_3_exons|my_multi_exon_contig_1|+|100_exon_2 +my_multi_exon_contig_2 MetaEuk gene 101 723 402 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100 +my_multi_exon_contig_2 MetaEuk mRNA 101 723 402 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100 +my_multi_exon_contig_2 MetaEuk exon 101 430 235 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_0;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA +my_multi_exon_contig_2 MetaEuk CDS 101 430 235 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_CDS_0;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_0 +my_multi_exon_contig_2 MetaEuk exon 481 723 166 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_1;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_mRNA +my_multi_exon_contig_2 MetaEuk CDS 481 723 166 + . Target_ID=identical_all_2_exons;TCS_ID=identical_all_2_exons|my_multi_exon_contig_2|+|100_CDS_1;Parent=identical_all_2_exons|my_multi_exon_contig_2|+|100_exon_1 |