Mercurial > repos > devteam > gffread
diff gffread.xml @ 9:3e436657dcd0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffread commit 0d019235fcfc835b99d5651b0bc4fd0da06707ac
| author | iuc |
|---|---|
| date | Fri, 15 Dec 2023 19:39:24 +0000 |
| parents | 154d00cbbf2d |
| children |
line wrap: on
line diff
--- a/gffread.xml Sat Sep 25 15:38:31 2021 +0000 +++ b/gffread.xml Fri Dec 15 19:39:24 2023 +0000 @@ -1,12 +1,9 @@ <tool id="gffread" name="gffread" version="@GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>Filters and/or converts GFF3/GTF2 records</description> - <xrefs> - <xref type="bio.tools">gffread</xref> - </xrefs> <macros> <!-- the version of this tool must not be lowered since in the past 2.x was used lets use small increments and hope that gffread catches up one day --> - <token name="@GALAXY_TOOL_VERSION@">2.2.1.3</token> + <token name="@GALAXY_TOOL_VERSION@">2.2.1.4</token> <token name="@TOOL_VERSION@">0.12.7</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="fasta_output_select"> @@ -55,6 +52,9 @@ </param> </xml> </macros> + <xrefs> + <xref type="bio.tools">gffread</xref> + </xrefs> <requirements> <requirement type="package" version="@TOOL_VERSION@">gffread</requirement> </requirements> @@ -116,13 +116,13 @@ #echo ' ' + ' '.join(str($reference_genome.fa_outputs).split(',')) #end if #end if + #if $gffs.gff_fmt != 'none': #if $gffs.gff_fmt != 'bed' and $gffs.tname: -t '$gffs.tname' #end if #if $gffs.gff_fmt == 'gff': - ## TODO bug 'gft' -> 'gtf' - #if $input.datatype.file_ext == 'gft': + #if $input.datatype.file_ext == 'gtf': $gffs.ensembl #end if #end if @@ -132,6 +132,8 @@ --bed #end if -o output.$gffs.gff_fmt + #else if 'fa_outputs' not in $reference_genome or '.fa' not in str($reference_genome['fa_outputs']) + -o output.gff #end if ## Missing options @@ -253,11 +255,10 @@ <conditional name="reference_genome"> <param name="source" type="select" label="Reference Genome" help="NOTE: Required for fasta outputs"> <option value="none">none</option> - <option value="cached"></option> + <option value="cached">Cached reference data</option> <option value="history">From your history</option> </param> - <when value="none"> - </when> + <when value="none"/> <when value="cached"> <param argument="-g" name="fasta_indexes" type="select" label="Source FASTA Sequence"> <options from_data_table="all_fasta"/> @@ -280,8 +281,7 @@ <option value="gtf">GTF</option> <option value="bed">BED</option> </param> - <when value="none"> - </when> + <when value="none"/> <when value="gff"> <param argument="-L" name="ensembl" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Ensembl GTF to GFF3 conversion" help=""/> <expand macro="trackname" /> @@ -289,8 +289,7 @@ <when value="gtf"> <expand macro="trackname" /> </when> - <when value="bed"> - </when> + <when value="bed"/> </conditional> <param argument="-F" name="full_gff_attribute_preservation" type="boolean" truevalue="-F" falsevalue="" checked="false" @@ -303,7 +302,8 @@ </inputs> <outputs> <data name="output_gff" format="gff3" metadata_source="input" label="${tool.name} on ${on_string}: gff3" from_work_dir="output.gff"> - <filter>gffs['gff_fmt'] == 'gff'</filter> + <!-- output gff also if the user deselected all outputs: none is selected and all .fa outputs are disabled --> + <filter>gffs['gff_fmt'] == 'gff' or (gffs['gff_fmt'] == 'none' and ('fa_outputs' not in reference_genome or '.fa' not in str(reference_genome['fa_outputs'])))</filter> </data> <data name="output_gtf" format="gtf" metadata_source="input" label="${tool.name} on ${on_string}: gtf" from_work_dir="output.gtf"> <filter>gffs['gff_fmt'] == 'gtf'</filter> @@ -329,17 +329,67 @@ <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> <param name="gff_fmt" value="gff"/> <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> + </test> + <!-- mapping --> + <test expect_num_outputs="1"> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <param name="gff_fmt" value="gff"/> + <param name="chr_replace" ftype="tabular" value="chr_replace"/> + <output name="output_gff" ftype="gff3"> + <assert_contents> + <has_n_lines n="314"/> + <has_line_matching expression="^chr.*"/> + <has_line_matching expression="^1.*" negate="true"/> + </assert_contents> + </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> + </test> + <!-- none output and all .fa outputs deselected .. gff is produced anyway, since we need one output --> + <test expect_num_outputs="1"> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> + </test> + <!-- test ensemble gtf to gff conversion --> + <test expect_num_outputs="1"> + <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> + <conditional name="gffs"> + <param name="gff_fmt" value="gff"/> + <param name="ensembl" value="true"/> + <param name="tname" value="track name"/> + </conditional> + <output name="output_gff" file="Homo_sapiens.GRCh37_19.71_ensemble.gff3" ftype="gff3" lines_diff="4" /> + <assert_command> + <has_text text="-L"/> + <has_text text="-t 'track name'"/> + </assert_command> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> <param name="gff_fmt" value="gff"/> <output name="output_gff" file="Homo_sapiens.GRCh37_19.71.gff3" ftype="gff3" lines_diff="4" /> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="ecoli-k12.gff3"/> <param name="gff_fmt" value="gff"/> <param name="full_gff_attribute_preservation" value="-F"/> <output name="output_gff" file="ecoli-k12.processed.gff3" ftype="gff3" lines_diff="4" /> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <!-- bed output --> <test expect_num_outputs="1"> @@ -351,6 +401,9 @@ <has_n_columns n="13"/> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <!-- bed input and test tname --> <test expect_num_outputs="1"> @@ -365,6 +418,9 @@ <has_text text="track name"/> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> @@ -377,6 +433,9 @@ <has_text text="ENST00000382683" /> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> @@ -390,6 +449,9 @@ <has_text text="ENST00000382683" /> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> @@ -403,6 +465,9 @@ <has_text text="ENST00000382683" /> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="4"> <param name="input" ftype="gtf" value="Homo_sapiens.GRCh37_19.71.gtf"/> @@ -436,6 +501,9 @@ <has_text text="MDFGLALLLAGLLGLLLGQSLQVKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAV" /> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> <test expect_num_outputs="1"> <param name="input" ftype="gtf" value="stop_codons.gtf"/> @@ -448,6 +516,9 @@ <has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" /> </assert_contents> </output> + <assert_stdout> + <has_n_lines n="0"/> + </assert_stdout> </test> </tests> <help>