Mercurial > repos > iuc > metaeuk_easy_predict
changeset 2:be6bbdeafcb8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaeuk commit 3309bdde7b03c5c250a020b0aee221133d9ea79b"
author | iuc |
---|---|
date | Thu, 21 Oct 2021 16:10:35 +0000 |
parents | f91548912113 |
children | 860f8836c936 |
files | metaeuk_easy_predict.xml test-data/output.gff test-data/output_w_frag_coords.fasta |
diffstat | 3 files changed, 33 insertions(+), 2 deletions(-) [+] |
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--- a/metaeuk_easy_predict.xml Sun Jul 18 17:41:54 2021 +0000 +++ b/metaeuk_easy_predict.xml Thu Oct 21 16:10:35 2021 +0000 @@ -1,7 +1,10 @@ <tool id="metaeuk_easy_predict" name="MetaEuk Easy Predict" version="@TOOL_VERSION@+galaxy0"> <description>High-throughput gene discovery and annotation for large-scale eukaryotic metagenomics</description> + <xrefs> + <xref type="bio.tools">MetaEuk</xref> + </xrefs> <macros> - <token name="@TOOL_VERSION@">4.a0f584d</token> + <token name="@TOOL_VERSION@">5.34c21f2</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">metaeuk</requirement> @@ -22,7 +25,9 @@ --max-intron '${adv.max_intron}' --min-intron '${adv.min_intron}' #end if + --write-frag-coords $write_frag_coords && mv output.fasta.codon.fas '$output' + && mv output.fasta.gff '$gff_output' ]]></command> <inputs> <param name="contigs" type="data" format="fasta" label="Contigs to search again" /> @@ -43,9 +48,14 @@ <when value="no"> </when> </conditional> + <param name="write_frag_coords" type="select" value="0" label="Write the contig coords of the stop-to-stop fragment in which putative exon lies" help="The fragment coordinates in square brackets refer to the original fragment in which the exon was found." > + <option value="0">Yes</option> + <option value="1">No</option> + </param> </inputs> <outputs> <data name="output" format="fasta" /> + <data name="gff_output" format="gff" /> </outputs> <tests> @@ -53,10 +63,12 @@ <param name="contigs" ftype="fasta" value="contigs.fna" /> <param name="query" ftype="fasta" value="proteins.faa" /> <output name="output" ftype="fasta" value="output.fasta" /> + <output name="gff_output" ftype="gff" value="output.gff" /> </test> <test> <param name="contigs" ftype="fasta" value="contigs.fna" /> <param name="query" ftype="fasta" value="proteins.faa" /> + <param name="write_frag_coords" value="1" /> <conditional name="adv"> <param name="adv_options" value="yes" /> <param name="max_intron" value="1000" /> @@ -64,7 +76,8 @@ <assert_command> <has_text text="--max-intron '1000'" /> </assert_command> - <output name="output" ftype="fasta" value="output.fasta" /> + <output name="output" ftype="fasta" value="output_w_frag_coords.fasta" /> + <output name="gff_output" ftype="gff" value="output.gff" /> </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.gff Thu Oct 21 16:10:35 2021 +0000 @@ -0,0 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_w_frag_coords.fasta Thu Oct 21 16:10:35 2021 +0000 @@ -0,0 +1,4 @@ +>identical_all_3_exons|my_multi_exon_contig_1|+|629|7.362e-187|3|100|1141|[82]100[100]:[468]429[429]:330[330]|[477]480[480]:[884]881[881]:402[402]|[866]944[968]:[1147]1141[1141]:198[174] +ATGACTTTATGCGCAGGTTTTGACCCTAATCGATTTTTGCCCATCGTTCTCGACGTTGGCACCAACAATGAAACCCATCGTAAAAATCATCAATACATGGGTTTAAGAAAGGACCGTGTTCACGGTGAGCAGTATGACATCTTTTTGGAGAACGTTATTAAAGCCATTCGTGAAGTCTTTCCCGAGGCCTTTATTCACTTTGAGGATTTCGGACTTAAAAATGCCAAAAGGATTTTAGACCACTATCGTCCTAATATTGCCTGTTTTAACGATGATATCCAGGGCACCGGTGCTGTAGCACTGGCCGCCATTATAGGCGCCCTTCATGTTACGAAGTCTCCCTTAACCGAGCAGCGCATCATGATCTTTGGTGCTGGTACTGCTGGTGTTGGTATCGCCAACCAAATTGTCGCTGGTATGGTGACAGATGGCCTTTCATTAGGTAAGGCTAGAGATAATCTTTTCATGATTGATCGATGCGGTTTGCTTCTGGAGAGACATGCTAAGATTGCTACTGATGGACAAAAGCCATTTTTGAAGAAGGACTCAGACTTTAAGGAAGTCCCTTCTGGAGACATTGATTTAGAGACTGCTATTTCACTAATCAAACCCACTGTTCTTCTGGGGTGCTCCGGTCAACCTGGAAAATTTACAGAAAAGGCCATTCGTGAAATGAGCAAGCATGTCAAACATCCCATCATCTTCCCAATCTCTAACCCCACCACTCTCATGAAGCCCGTTCAAATTGACGAATGGTCTAATGGTAAAGCTTTGATGGCAACTGGTTCTCCACTTCCTCCTCTCACACGTAATGGTAAAGAATATGTGATTTCTCAATGCAATAATGCTCTTCTTTACCCTGCTCTAGGTGTTGCATGTGTGTTATCCCGTTGCAAATTGTTGAGC +>identical_all_2_exons|my_multi_exon_contig_2|+|402|1.588e-118|2|100|722|[82]100[100]:[468]429[429]:330[330]|[477]480[480]:[740]722[722]:243[243] +ATGACTTTATGCGCAGGTTTTGACCCTAATCGATTTTTGCCCATCGTTCTCGACGTTGGCACCAACAATGAAACCCATCGTAAAAATCATCAATACATGGGTTTAAGAAAGGACCGTGTTCACGGTGAGCAGTATGACATCTTTTTGGAGAACGTTATTAAAGCCATTCGTGAAGTCTTTCCCGAGGCCTTTATTCACTTTGAGGATTTCGGACTTAAAAATGCCAAAAGGATTTTAGACCACTATCGTCCTAATATTGCCTGTTTTAACGATGATATCCAGGGCACCGGTGCTGTAGCACTGGCCGCCATTATAGGCGCCCTTCATGTTGATGGAATGCTGAAAGCAGCTTCCGATGCTTTGGCCACTGTTCCTAGATCTTTGTTTGTCGCCGATGAAGCTCTCTTGCCAGATCTGGACAATGCTCGAGAAATCTCTCGTCACATCGTTTTTGCGGTTTTGAAGCAAGCCATTTCTGAAGGAATGAGCACAGTGGATTTACCCAAAGATGATGCCAAGTTGAAGGAATGGATTATTGAACGAGAATGGAACCCTGAATACAGGAATTTTGTA