agat: agat.xml comparison

comparison agat.xml @ 2:e009d8260be2 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae

author	bgruening
date	Thu, 07 Sep 2023 05:29:24 +0000
parents	f7c0a0030254
children	a6318f87f2cd

comparison

equal deleted inserted replaced

-:6d8444408ff1
+:e009d8260be2
 <expand macro="requirements" />
 <version_command>agat_sq_stat_basic.pl --version</version_command>
 <command detect_errors="exit_code"><![CDATA[
 #if $tool.selector == 'fix'
 @input_annotation_single@
-agat_convert_sp_gxf2gxf.pl -gff $input_annotation --output 'output.gff' &&
+agat_convert_sp_gxf2gxf.pl
-cat 'output.gff' > '${annotation_gff}'
+--gxf $input_annotation
+--config $agat_configfile
+--output 'output' &&
+cat 'output' > '${annotation}'
 #else if $tool.selector == 'convert_GFF2GTF'
 @input_annotation_single@
-agat_convert_sp_gff2gtf.pl --gff $input_annotation --gtf_version $tool.gtf_version --output 'output.gtf' &&
+agat_convert_sp_gff2gtf.pl
+--gff $input_annotation
+--gtf_version $tool.gtf_version
+--output 'output.gtf' &&
 cat 'output.gtf' > '${annotation_gtf}'
 #else if $tool.selector == 'convert_GTF2GFF'
 @input_annotation_single@
-agat_convert_sp_gxf2gxf.pl --gff $input_annotation --output 'output.gff' &&
+agat_convert_sp_gxf2gxf.pl
+--gff $input_annotation
+--output 'output.gff' &&
 cat 'output.gff' > '${annotation_gff}'
 #else if $tool.selector == 'compare'
 @input_annotation_double@
-agat_sp_compare_two_annotations.pl --gff1 $input1 --gff2 $input2 --output 'temp_output' &&
+agat_sp_compare_two_annotations.pl
+--gff1 $input1
+--gff2 $input2
+--output 'temp_output' &&
 cat 'temp_output' > '${stats_output}'
 #else if $tool.selector == 'extract'
 @input_annotation_single@
 @input_reference@
 agat_sp_extract_sequences.pl
 --output '${sequence_output}'
 #else if $tool.selector == 'functional_analysis'
 @input_annotation_single@
 @input_reference@
 mkdir -p './statistics' &&
-agat_sp_statistics.pl
+agat_sp_functional_statistics.pl
 --gff $input_annotation
 --gs $ref_genome
 --output 'temp_output' &&
-cat 'temp_output' > '$stats_output'
+cat 'temp_output/gene@transcript/table_per_feature_type.txt' > '$stats_output'
 #else if  $tool.selector == 'merge_annotations'
 @input_annotation_double@
-agat_sp_merge_annotations.pl -gff $input1 --gff $input2 --output 'temp_output' &&
+agat_sp_merge_annotations.pl
-cat 'temp_output' > '${annotation_gff}'
+--gff $input1
+--gff $input2
+--config $agat_configfile
+--output 'output' &&
+cat 'output' > '${annotation}'
 #else if $tool.selector == 'annotation_statistics'
 @input_annotation_single@
 @input_reference@
-agat_sp_statistics.pl --gff $input_annotation --gs $ref_genome -d --output 'temp_output' &&
+agat_sp_statistics.pl
+--gff $input_annotation
+--gs $ref_genome
+-d
+--output 'temp_output' &&
 cat 'temp_output' > '$stats_output'
 #else if $tool.selector == 'filter_feature_fasta'
 @input_annotation_single@
 @input_reference@
-agat_sq_filter_feature_from_fasta.pl --gff $input_annotation --fasta $ref_genome --output 'temp_output' &&
+agat_sq_filter_feature_from_fasta.pl
-cat 'temp_output' > '${features_filtered}'
+--gff $input_annotation
+--fasta $ref_genome
+--config $agat_configfile
+--output 'output' &&
+cat 'output' > '${annotation}'
 #else if $tool.selector == 'complement'
 @input_annotation_double@
-agat_sp_complement_annotations.pl --ref $input1 --add $input2 --size_min $tool.size_min --output 'temp_output' &&
+agat_sp_complement_annotations.pl
-cat 'temp_output' > '${annotation_gff}'
+--ref $input1
+--add $input2
+--size_min $tool.size_min
+--config $agat_configfile
+--output 'temp_output' &&
+cat 'temp_output' > '${annotation}'
+#else if $tool.selector == 'splice_sites'
+@input_annotation_single@
+agat_sp_add_splice_sites.pl
+--gff $input_annotation
+--config $agat_configfile
+--output 'output' &&
+cat 'output' > '${annotation}'
 #end if
 ]]>
 </command>
+<configfiles>
+<configfile name="agat_configfile"><![CDATA[
+#if $tool.selector in ['fix','merge_annotations','complement','splice_sites','filter_feature_fasta']
+---
+output_format: $tool.output_format.selector
+#if $tool.output_format.selector == "GFF"
+gff_output_version: $tool.output_format.version
+gtf_output_version: relax
+#else
+gff_output_version: 3
+gtf_output_version: $tool.output_format.version
+#end if
+verbose: 1
+progress_bar: true
+log: true
+debug: false
+tabix: false
+merge_loci: $tool.merge_loci
+throw_fasta: false
+force_gff_input_version: 0
+create_l3_for_l2_orphan: $tool.create_exon
+locus_tag:
+- locus_tag
+- gene_id
+prefix_new_id: nbis
+check_sequential: true
+check_l2_linked_to_l3: true
+check_l1_linked_to_l2: true
+remove_orphan_l1: true
+check_all_level3_locations: true
+check_cds: true
+check_exons: true
+check_utrs: true
+check_all_level2_locations: true
+check_all_level1_locations: true
+check_identical_isoforms: true
+#end if
+]]></configfile>
+</configfiles>
 <inputs>
 <conditional name="tool">
 <param name="selector" type="select" label="AGAT tool selector" help="As AGAT is a toolkit, it contains a lot of tools. If any of them is missing, please contact the server admin.">
+<option value="splice_sites">Add splice sites</option>
 <option value="annotation_statistics">Annotation statistics (agat_sp_statistics.pl)</option>
 <option value="compare">Compare annotation files (agat_sp_compare_two_annotations.pl)</option>
 <option value="complement">Complement annotation file (agat_sp_complement_annotations.pl)</option>
 <option value="extract">Extract sequences (agat_sp_extract_sequences.pl)</option>
 <option value="convert_GFF2GTF">GFF to GTF format conversion (agat_convert_sp_gff2gtf.pl)</option>
 <option value="gene">Gene</option>
 <option value="transcript">Transcript</option>
 <option value="exon">Exon</option>
 <option value="cds">CDS</option>
 <option value="trna">tRNA</option>
-<option value="three_prime_utr">3' UTR</option>
+<option value="three_prime_utr">3 UTR</option>
-<option value="five_prime_utr">5' UTR</option>
+<option value="five_prime_utr">5 UTR</option>
 </param>
 <param argument="--mrna" type="boolean" truevalue="--mrna" falsevalue="" checked="false" label="Extract mRNA sequences" help=" This extract the mrna
 sequence (i.e transcribed sequence (devoid of introns, but containing untranslated exons))." />
 <param argument="--cdna" type="boolean" truevalue="--cdna" falsevalue="" checked="false" label="Extract the cDNA sequence"
 help=" This extract the cdna sequence (i.e reverse complement of the mRNA: transcribed sequence (devoid of introns, but
 help=" This option allows removing the translation of the final stop codons that is represented by the '*' character. This character can be
 disturbing for many programs (e.g interproscan)" />
 <param argument="--clean_internal_stop" type="boolean" truevalue="--clean_internal_stop" falsevalue="" checked="false" label="Clean internal
 stop codons" help="The Clean Internal Stop option allows replacing the translation of the stop codons present among the sequence that is
 represented by the '*' character by . This character can be disturbing for many programs (e.g interproscan)" />
-<param argument="--upstream" type="integer" min="0" value="" optional="true" label="Upstream nucleotides" help="It will take that number of nucleotide in more at the 5' extremity." />
+<param argument="--upstream" type="integer" min="0" value="" optional="true" label="Upstream nucleotides" help="It will take that number of nucleotide in more at the 5 extremity." />
 <param argument="--downstream" type="integer" min="0" value="" optional="true" label="Downstream nucleotides" help="It will take that number of downstream nucleotides." />
 <param argument="--full" type="boolean" truevalue="--full" falsevalue="" checked="false" label="Full" help="This option allows dealing
 with feature that may span over several locations like CDS or exon, in order to extract the full sequence from the start extremity
 of the first chunck to the end extremity of the last chunk. The use of that option with '--type exon' will extract the pre-mRNA
 sequence (i.e with introns). Use of that option on CDS will give the pre-mRNA without the untraslated regions (UTRs). " />
 <expand macro="ANNOTATION_INPUT" format="gtf"/>
 </when>
 <when value="filter_feature_fasta">
 <expand macro="ANNOTATION_INPUT" />
 <expand macro="REFERENCE_FASTA"/>
+<expand macro="AGAT_CONFIG"/>
 </when>
 <when value="fix">
 <expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
+<expand macro="AGAT_CONFIG"/>
 </when>
 <when value="functional_analysis">
 <expand macro="ANNOTATION_INPUT" format="gff,gtf,gff3,gff3.gz"/>
 <expand macro="REFERENCE_FASTA"/>
 </when>
 <when value="merge_annotations">
 <param argument="--gff1" name="input_annotation1" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation file 1" help="Input GTF/GFF file" />
 <param argument="--gff2" name="input_annotation2" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation file 2" help="Input GTF/GFF file" />
+<expand macro="AGAT_CONFIG"/>
 </when>
 <when value="complement">
 <param argument="--ref" name="input_annotation1" type="data" format="gff,gtf,gff3,gff3.gz" label="Reference annotaiton" help="Reference GTF/GFF file" />
 <param argument="--add" name="input_annotation2" type="data" format="gff,gtf,gff3,gff3.gz" label="Annotation to complement" help="Annotation file you would like to use to complement the reference annotation." />
 <param argument="--size_min" type="integer" min="0" value="0" label="Minimun CDS size" help="Option to keep the non-overlping gene only if the CDS size (in nucleotide) is over the minimum
 size defined. Default = 0 that means all of them are kept." />
+<expand macro="AGAT_CONFIG"/>
+</when>
+<when value="splice_sites">
+<expand macro="ANNOTATION_INPUT" format="gff,gff3,gff3.gz"/>
+<expand macro="AGAT_CONFIG"/>
 </when>
 </conditional>
 </inputs>
 <outputs>
 <data name="annotation_gff" format="gff" label="${tool.name} on ${on_string}: annotation file (GFF)">
-<filter>tool['selector'] not in ['annotation_statistics','extract','functional_analysis','compare','convert_GFF2GTF','filter_feature_fasta']</filter>
+<filter>tool['selector'] == 'convert_GTF2GFF'</filter>
 </data>
 <data name="annotation_gtf" format="gtf" label="${tool.name} on ${on_string}: annotation file (GTF)">
 <filter>tool['selector'] == 'convert_GFF2GTF'</filter>
 </data>
-<data name="features_filtered" format="tabular" label="${tool.name} on ${on_string}: filtered results">
+<data name="annotation" format="gff" label="${tool.name} on ${on_string}: annotation file">
-<filter>tool['selector'] == 'filter_feature_fasta'</filter>
+<filter>tool['selector'] in ['fix','merge_annotations','complement','filter_feature_fasta','splice_sites','bam2gff']</filter>
+<change_format>
+<when input="output_format.selector" value="GTF" format="gtf" />
+</change_format>
 </data>
 <data name="sequence_output" format="fasta" label="${tool.name} on ${on_string}: FASTA file">
 <filter>tool['selector'] =='extract'</filter>
 </data>
 <data name="stats_output" format="txt" label="${tool.name} on ${on_string}: stats file">
 <param name="source" value="history"/>
 <param name="history_item" value="genome.fasta.gz"/>
 </conditional>
 </conditional>
 <output name="stats_output" file="test01_stats.txt" ftype="txt"/>
-<output_collection name="distribution_plots_woiso" type="list" count="4">
-<element name="transcriptClass_cds" file="test01_plot2.pdf" ftype="pdf" compare="sim_size" delta="100"/>
-</output_collection>
 <output_collection name="distribution_plots_wiso" type="list" count="4">
 <element name="transcriptClass_cds" file="test01_plot1.pdf" ftype="pdf" compare="sim_size" delta="100"/>
 </output_collection>
 </test>
 <!-- Test 02: extract sequences -->
 <param name="input_annotation1" value="annotation.gtf"/>
 <param name="input_annotation2" value="annotation_small.gtf"/>
 </conditional>
 <output name="stats_output" file="test03.txt" ftype="txt" lines_diff="2"/>
 </test>
-<!-- Test 04: comlement annotation -->
+<!-- Test 04: complement annotation -->
 <test expect_num_outputs="1">
 <conditional name="tool">
 <param name="selector" value="complement"/>
 <param name="input_annotation1" value="annotation_small.gtf" ftype="gtf"/>
 <param name="input_annotation2" value="annotation_unique.gtf" ftype="gtf"/>
 <param name="size_min" value="10"/>
+<conditional name="output_format">
+<param name="selector" value="gff"/>
+<param name="version" value="3"/>
+</conditional>
 </conditional>
 <output name="annotation_gff" file="test04.gff" ftype="gff"/>
 </test>
 <!-- Test 05: Convert GFF2GTF -->
 <test expect_num_outputs="1">
 <conditional name="reference_genome">
 <param name="source" value="history"/>
 <param name="history_item" value="genome.fasta.gz"/>
 </conditional>
 </conditional>
-<output name="features_filtered" file="test07.tabular" ftype="tabular"/>
+<output name="annotation" file="test07.gff" ftype="gff"/>
 </test>
 <!-- Test 08: Fix annotation file -->
 <test expect_num_outputs="1">
 <conditional name="tool">
 <param name="selector" value="fix"/>
 <conditional name="tool">
 <param name="selector" value="merge_annotations"/>
 <param name="input_annotation1" value="annotation_small.gtf"/>
 <param name="input_annotation2" value="annotation_unique.gtf"/>
 </conditional>
+<conditional name="output_format">
+<param name="selector" value="gff"/>
+<param name="version" value="3"/>
+</conditional>
 <output name="annotation_gff" file="test10.gff" ftype="gff"/>
 </test>
 <!-- Test 11: Test compressed files -->
 <test expect_num_outputs="1">
 <conditional name="tool">
 </conditional>
 <assert_stdout>
 <has_text text="Job done" />
 </assert_stdout>
 </test>
+<!-- Test 13: Add splicing sites -->
+<test expect_num_outputs="1">
+<conditional name="tool">
+<param name="selector" value="splice_sites"/>
+<param name="gff" value="test04.gff" ftype="gff"/>
+</conditional>
+<output name="annotation" file="test13.gff" ftype="gff"/>
+</test>
 </tests>
 <help><![CDATA[
 .. class:: infomark

Mercurial > repos > bgruening > agat

comparison agat.xml @ 2:e009d8260be2 draft