Mercurial > repos > iuc > aegean_gaeval
diff gaeval.xml @ 1:8dc7512c9dc9 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit 669dd4d406e86aee7d83e7420dced981c180d805
| author | iuc |
|---|---|
| date | Sun, 11 Feb 2024 11:30:13 +0000 |
| parents | 1dd7adc21b6d |
| children |
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--- a/gaeval.xml Sun Jan 03 14:59:26 2021 +0000 +++ b/gaeval.xml Sun Feb 11 11:30:13 2024 +0000 @@ -1,92 +1,92 @@ -<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@" profile="20.01"> +<tool id="aegean_gaeval" name="AEGeAn GAEVAL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> <description> compute coverage and integrity scores for gene models using transcript alignments.</description> <macros> <import>macros.xml</import> </macros> - <expand macro='xrefs'/> - <expand macro='edam_ontology'/> - <expand macro='requirements'/> + <expand macro="edam_ontology"/> + <expand macro="xrefs"/> + <expand macro="requirements"/> <version_command>gaeval --version</version_command> - <command detect_errors='exit_code'> + <command detect_errors="exit_code"> <![CDATA[ - gaeval '$alignmentgff3' '$genesgff3' + gaeval "$alignmentgff3" "$genesgff3" -a $weights.alpha -b $weights.beta -g $weights.gamma -e $weights.epsilon -c $expected.expcds -5 $expected.exp5putr - -3 $expected.exp3putr > '$output' + -3 $expected.exp3putr > "$output" ]]> </command> <inputs> - <param name='alignmentgff3' type='data' format='gff3' label='Alignment GFF3 file' /> - <param name='genesgff3' type='data' format='gff3' label='Genes GFF3 file'/> + <param name="alignmentgff3" type="data" format="gff3" label="Alignment GFF3 file" /> + <param name="genesgff3" type="data" format="gff3" label="Genes GFF3 file"/> <!-- Weight options --> - <section name='weights' - title='Weights for calculating integrity score' - expanded='False'> - <param argument='--alpha' type='float' - min='0' max='1' value='0.6' - label='Introns confirmed, or % expected CDS lenght for single-exon genes' - help='The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. '/> - <param argument='--beta' type='float' - min='0' max='1' value='0.3' - label='Exon coverage' - help='Overall percentage of individual exons spanned by at least one sequencing read.'/> - <param argument='--gamma' type='float' - min='0' max='1' value='0.05' - label='% expected 5’ UTR length' - help='The ratio of the observed 5’ UTR length to the expected 5’ UTR length.'/> - <param argument='--epsilon' type='float' - min='0' max='1' value='0.05' - label='% expected 3’ UTR lenght' - help='The ratio of the observed 3’ UTR length to the expected 3’ UTR length.'/> + <section name="weights" + title="Weights for calculating integrity score" + expanded="False"> + <param argument="--alpha" type="float" + min="0" max="1" value="0.6" + label="Introns confirmed, or % expected CDS lenght for single-exon genes" + help="The percentage of introns confirmed by an alignment gap; for single-exon gene predictions lacking introns, it represents the ratio of the observed CDS length to the expected CDS length. "/> + <param argument="--beta" type="float" + min="0" max="1" value="0.3" + label="Exon coverage" + help="Overall percentage of individual exons spanned by at least one sequencing read."/> + <param argument="--gamma" type="float" + min="0" max="1" value="0.05" + label="% expected 5’ UTR length" + help="The ratio of the observed 5’ UTR length to the expected 5’ UTR length."/> + <param argument="--epsilon" type="float" + min="0" max="1" value="0.05" + label="% expected 3’ UTR lenght" + help="The ratio of the observed 3’ UTR length to the expected 3’ UTR length."/> </section> <!-- Expected feature lenght options --> - <section name='expected' - title='Expected feature lenghts for calculating integrity score' - expanded='False'> - <param name='expcds' type='integer' - min='0' max='1000' value='400' - label='Expected CDs length (in bp) (-c)' /> - <param name='exp5putr' type='integer' - min='0' max='1000' value='200' - label='Expected 5’ UTR length (-5)' /> - <param name='exp3putr' type='integer' - min='0' max='1000' value='100' - label='Expected 3’ UTR length (-3)' /> + <section name="expected" + title="Expected feature lenghts for calculating integrity score" + expanded="False"> + <param name="expcds" type="integer" + min="0" max="1000" value="400" + label="Expected CDs length (in bp) (-c)" /> + <param name="exp5putr" type="integer" + min="0" max="1000" value="200" + label="Expected 5’ UTR length (-5)" /> + <param name="exp3putr" type="integer" + min="0" max="1000" value="100" + label="Expected 3’ UTR length (-3)" /> </section> </inputs> <outputs> - <data name='output' format='tabular' /> + <data name="output" format="tabular" /> </outputs> <tests> <test expect_num_outputs="1"> - <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <output name='output' file='gaeval_output_test1.txt'/> + <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <output name="output" file="gaeval_output_test1.txt"/> </test> <test expect_num_outputs="1"> - <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='weights'> - <param name='alpha' value='0.5'/> - <param name='beta' value='0.4'/> - <param name='gamma' value='0.05'/> - <param name='epsion' value='0.05'/> + <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="weights"> + <param name="alpha" value="0.5"/> + <param name="beta" value="0.4"/> + <param name="gamma" value="0.05"/> + <param name="epsion" value="0.05"/> </section> - <output name='output' file='gaeval_output_test2.txt'/> + <output name="output" file="gaeval_output_test2.txt"/> </test> <test expect_num_outputs="1"> - <param name='alignmentgff3' value='TAIR10_GFF3_alignment.gff'/> - <param name='genesgff3' value='TAIR10_GFF3_genes.gff'/> - <section name='expected'> - <param name='expcds' value='20'/> - <param name='exp5putr' value='150'/> - <param name='exp3putr' value='120'/> + <param name="alignmentgff3" value="TAIR10_GFF3_alignment.gff" ftype="gff3"/> + <param name="genesgff3" value="TAIR10_GFF3_genes.gff" ftype="gff3"/> + <section name="expected"> + <param name="expcds" value="20"/> + <param name="exp5putr" value="150"/> + <param name="exp3putr" value="120"/> </section> - <output name='output' file='gaeval_output_test3.txt' lines_diff='2'/> + <output name="output" file="gaeval_output_test3.txt" lines_diff="2"/> </test> </tests> @@ -126,5 +126,5 @@ ]]> </help> - <expand macro='citations'/> + <expand macro="citations"/> </tool>