| Next changeset 1:66310cfc17dd (2024-02-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tsebra commit 4bd553d5f49cca7b7acba0ad05fcbebb9a760a4f |
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added:
macros.xml test-data/braker.gtf test-data/hintsfile.gff test-data/output.gtf test-data/output.txt tsebra.xml |
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| diff -r 000000000000 -r 174c63ee0150 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Oct 30 15:35:25 2023 +0000 |
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| @@ -0,0 +1,8 @@ +<macros> + <token name="@TOOL_VERSION@">1.1.2</token> + <xml name="citation"> + <citations> + <citation type="doi">/10.1186/s12859-021-04482-0</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 174c63ee0150 test-data/braker.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/braker.gtf Mon Oct 30 15:35:25 2023 +0000 |
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| b'@@ -0,0 +1,10700 @@\n+scaffold_1\tAUGUSTUS\tgene\t384\t1158\t.\t-\t.\tg1\n+scaffold_1\tAUGUSTUS\ttranscript\t384\t1158\t0.97\t-\t.\tg1.t1\n+scaffold_1\tAUGUSTUS\tstop_codon\t384\t386\t.\t-\t0\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\tCDS\t384\t800\t0.97\t-\t0\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\texon\t384\t800\t.\t-\t.\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\tintron\t801\t879\t1\t-\t.\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\tCDS\t880\t1158\t1\t-\t0\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\texon\t880\t1158\t.\t-\t.\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\tstart_codon\t1156\t1158\t.\t-\t0\ttranscript_id "g1.t1"; gene_id "g1";\n+scaffold_1\tAUGUSTUS\tgene\t4178\t5370\t.\t+\t.\tg2\n+scaffold_1\tAUGUSTUS\ttranscript\t4178\t5370\t0.82\t+\t.\tg2.t1\n+scaffold_1\tAUGUSTUS\tstart_codon\t4178\t4180\t.\t+\t0\ttranscript_id "g2.t1"; gene_id "g2";\n+scaffold_1\tAUGUSTUS\tCDS\t4178\t4203\t1\t+\t0\ttranscript_id "g2.t1"; 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gene_id "g5581";\n+scaffold_2\tAUGUSTUS\tgene\t715281\t716118\t.\t-\t.\tg5582\n+scaffold_2\tAUGUSTUS\ttranscript\t715281\t716118\t0.88\t-\t.\tg5582.t1\n+scaffold_2\tAUGUSTUS\tstop_codon\t715281\t715283\t.\t-\t0\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\tCDS\t715281\t715849\t0.94\t-\t2\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\texon\t715281\t715849\t.\t-\t.\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\tintron\t715850\t716105\t0.88\t-\t.\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\tCDS\t716106\t716118\t0.88\t-\t0\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\texon\t716106\t716118\t.\t-\t.\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\tstart_codon\t716116\t716118\t.\t-\t0\ttranscript_id "g5582.t1"; gene_id "g5582";\n+scaffold_2\tAUGUSTUS\tgene\t716432\t717148\t.\t+\t.\tg5583\n+scaffold_2\tAUGUSTUS\ttranscript\t716432\t717148\t0.85\t+\t.\tg5583.t1\n+scaffold_2\tAUGUSTUS\tstart_codon\t716432\t716434\t.\t+\t0\ttranscript_id "g5583.t1"; gene_id "g5583";\n+scaffold_2\tAUGUSTUS\tCDS\t716432\t717148\t0.85\t+\t0\ttranscript_id "g5583.t1"; gene_id "g5583";\n+scaffold_2\tAUGUSTUS\texon\t716432\t717148\t.\t+\t.\ttranscript_id "g5583.t1"; gene_id "g5583";\n+scaffold_2\tAUGUSTUS\tstop_codon\t717146\t717148\t.\t+\t0\ttranscript_id "g5583.t1"; gene_id "g5583";\n' |
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| diff -r 000000000000 -r 174c63ee0150 test-data/hintsfile.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hintsfile.gff Mon Oct 30 15:35:25 2023 +0000 |
| b |
| b'@@ -0,0 +1,2582 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|
| b |
| diff -r 000000000000 -r 174c63ee0150 test-data/output.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.gtf Mon Oct 30 15:35:25 2023 +0000 |
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| b |
| diff -r 000000000000 -r 174c63ee0150 test-data/output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.txt Mon Oct 30 15:35:25 2023 +0000 |
| b |
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gene_id "g_595";\n+scaffold_2\tGeneMark.hmm3\tintron\t693091\t693175\t.\t+\t0\ttranscript_id "anno1.g5575.t2"; gene_id "g_595";\n+scaffold_2\tGeneMark.hmm3\tCDS\t693176\t693328\t.\t+\t0\ttranscript_id "anno1.g5575.t2"; gene_id "g_595";\n+scaffold_2\tGeneMark.hmm3\texon\t693176\t693328\t0\t+\t.\ttranscript_id "anno1.g5575.t2"; gene_id "g_595";\n+scaffold_2\tGeneMark.hmm3\tstop_codon\t693326\t693328\t.\t+\t0\ttranscript_id "anno1.g5575.t2"; gene_id "g_595";\n+scaffold_2\tAUGUSTUS\tgene\t695485\t698421\t.\t-\t.\tg_596\n+scaffold_2\tAUGUSTUS\ttranscript\t695485\t698421\t0.47\t-\t.\tanno1.g5576.t1\n+scaffold_2\tAUGUSTUS\tstop_codon\t695485\t695487\t.\t-\t0\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\tCDS\t695485\t697733\t0.95\t-\t2\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\texon\t695485\t697733\t.\t-\t.\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\tintron\t697734\t697808\t1\t-\t.\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\tCDS\t697809\t698421\t0.51\t-\t0\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\texon\t697809\t698421\t.\t-\t.\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\tstart_codon\t698419\t698421\t.\t-\t0\ttranscript_id "anno1.g5576.t1"; gene_id "g_596";\n+scaffold_2\tAUGUSTUS\tgene\t698522\t699409\t.\t-\t.\tg_597\n+scaffold_2\tAUGUSTUS\ttranscript\t698522\t699409\t0.55\t-\t.\tanno1.g5577.t1\n+scaffold_2\tAUGUSTUS\tstop_codon\t698522\t698524\t.\t-\t0\ttranscript_id "anno1.g5577.t1"; gene_id "g_597";\n+scaffold_2\tAUGUSTUS\tCDS\t698522\t699409\t0.55\t-\t0\ttranscript_id "anno1.g5577.t1"; gene_id "g_597";\n+scaffold_2\tAUGUSTUS\texon\t698522\t699409\t.\t-\t.\ttranscript_id "anno1.g5577.t1"; gene_id "g_597";\n+scaffold_2\tAUGUSTUS\tstart_codon\t699407\t699409\t.\t-\t0\ttranscript_id "anno1.g5577.t1"; gene_id "g_597";\n+scaffold_2\tAUGUSTUS\tgene\t716432\t717148\t.\t+\t.\tg_603\n+scaffold_2\tAUGUSTUS\ttranscript\t716432\t717148\t0.85\t+\t.\tanno1.g5583.t1\n+scaffold_2\tAUGUSTUS\tstart_codon\t716432\t716434\t.\t+\t0\ttranscript_id "anno1.g5583.t1"; gene_id "g_603";\n+scaffold_2\tAUGUSTUS\tCDS\t716432\t717148\t0.85\t+\t0\ttranscript_id "anno1.g5583.t1"; gene_id "g_603";\n+scaffold_2\tAUGUSTUS\texon\t716432\t717148\t.\t+\t.\ttranscript_id "anno1.g5583.t1"; gene_id "g_603";\n+scaffold_2\tAUGUSTUS\tstop_codon\t717146\t717148\t.\t+\t0\ttranscript_id "anno1.g5583.t1"; gene_id "g_603";\n' |
| b |
| diff -r 000000000000 -r 174c63ee0150 tsebra.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tsebra.xml Mon Oct 30 15:35:25 2023 +0000 |
| [ |
| @@ -0,0 +1,94 @@ +<?xml version="1.0"?> +<tool id="tsebra" name="TSEBRA" version="@TOOL_VERSION@+galaxy0" profile="21.05"> + <description>tanscript selector for BRAKER</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">tsebra</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + tsebra.py + + #if str( $gtf_file_param ) == "GTF": + -g '$gtf_input' + #elif str( $gtf_file_param ) == "KEEP_GTF": + -k '$gtf_input' + #end if + + #if $hint_file + -e '$hint_file' + #end if + #if $cfg_file + -c '$cfg_file' + #end if + + $ignore_tx_phase + #if $filter_exon + --filter_single_exon_genes + #end if + #if $score_tab + --score_tab '$output_tab' + #end if + + -o '$output' + ]]></command> + <inputs> + <param name="gtf_input" type="data" format="gtf" label="GTF input"/> + <param name="gtf_file_param" type="select" label="Choose the analysis parameter for the gtf file"> + <option value="GTF" selected="true">List of gene prediciton files</option> + <option value="KEEP_GTF">All transcripts from these gene sets will be included in the output</option> + </param> + <param name="hint_file" argument="-e" type="data" format="gff" optional="true" label="List of files containing extrinsic evidence"/> + <param name="cfg_file" argument="-c" type="data" format="txt" optional="true" label="Configuration file" help="Find the recommanded parameter at config/default.cfg"/> + <param name="score_tab" argument="-s" type="boolean" checked="false" label="Print the transcript scores as a table to the specified file"/> + <param name="ignore_transcrpts" type="boolean" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/> + <param name="filter_exon" type="boolean" label="Filter out all single-exon genes"/> + <param argument="--ignore_tx_phase" type="boolean" truevalue="--ignore_tx_phase" falsevalue="" label="Ignore the phase transcripts while detecting clusters of overlapping transcripts"/> + </inputs> + + <outputs> + <data name="output" format="gtf" label="TSEBRA on ${on_string}"/> + <data name="output_tab" format="txt" label="TSEBRA on ${on_string} : tab"> + <actions> + <action name="column_names" type="metadata" default="TX_ID,intron_support,stasto_support,s1,s2,s3,s4" /> + </actions> + <filter>score_tab</filter> + </data> + </outputs> + + <tests> + <test expect_num_outputs="1"> + <param name="gtf_input" value="braker.gtf" ftype="gtf"/> + <param name="hint_file" value="hintsfile.gff" ftype="gff"/> + <param name="score_tab" value="false"/> + <param name="gtf_file_param" value="GTF"/> + <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/> + </test> + + <test expect_num_outputs="2"> + <param name="gtf_input" value="braker.gtf" ftype="gtf"/> + <param name="hint_file" value="hintsfile.gff" ftype="gff"/> + <param name="score_tab" value="true"/> + <param name="gtf_file_param" value="GTF"/> + <output name="output" ftype="gtf" file="output.gtf" lines_diff="2"/> + <output name="output_tab" ftype="txt"> + <assert_contents> + <has_size value="32000" delta="300"/> + <has_text text="anno1;g1.t1"/> + <has_text text="anno1;g59.t1"/> + <has_text text="anno1;g169.t1"/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ + tsebra_ TSEBRA is a combinatorial tool that selects transcripts from genetic predictions based on support by extrinsic evidence + in the form of introns and start/stop codpns. This tool has been developed to combine BRAKER predictions. + + + .. _tsebra: https://github.com/Gaius-Augustus/TSEBRA + ]]></help> + <expand macro="citation"></expand> +</tool> |