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gffread: ensure empty stdout in tests (#5293)
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* gffread: ensure empty stdout in tests

xref #5028

* gffread: do not allow no outputs

it was possible to deselect all output datasets

add test for ref name replace

* fix TODO

* Bump tool version
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@bernt-matthias
bernt-matthias authored Dec 15, 2023
1 parent 3da34ac commit 0d01923
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Showing 2 changed files with 399 additions and 14 deletions.
99 changes: 85 additions & 14 deletions tools/gffread/gffread.xml
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Original file line number Diff line number Diff line change
@@ -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">
Expand Down Expand Up @@ -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>
Expand Down Expand Up @@ -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':
$gffs.ensembl
#end if
#end if
Expand All @@ -132,6 +132,8 @@
--bed
#end if
-o output.$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
Expand Down Expand Up @@ -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"/>
Expand All @@ -280,17 +281,15 @@
<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" />
</when>
<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"
Expand All @@ -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>
Expand All @@ -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 &#39;track name&#39;"/>
</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">
Expand All @@ -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">
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand All @@ -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"/>
Expand Down Expand Up @@ -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"/>
Expand All @@ -448,6 +516,9 @@
<has_text text="PLRGLHPRV*LQTPLERCPCWPPAGGTGGCPHCLLHLRLLQSPTPTALSEGGGAGTEAQPVTDVDPGRG*" />
</assert_contents>
</output>
<assert_stdout>
<has_n_lines n="0"/>
</assert_stdout>
</test>
</tests>
<help>
Expand Down
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