| Previous changeset 14:3061c8b029e5 (2022-08-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 617a2c388e73d6c93a2a1db9a58b914510052b69 |
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modified:
macros.xml quast.xml |
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| diff -r 3061c8b029e5 -r 72472698a2df macros.xml --- a/macros.xml Fri Aug 05 15:21:27 2022 +0000 +++ b/macros.xml Thu Mar 02 10:38:54 2023 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.2.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements> @@ -15,7 +15,7 @@ </xrefs> </xml> <xml name="gene_thresholds"> - <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> + <param argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/> </xml> <xml name="citations"> <citations> @@ -26,7 +26,28 @@ </citations> </xml> <xml name="min_identity_macros" token_value=""> - <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments - with IDY% less than 80.0% will be filtered regardless of this threshold. "/> + <param argument="--min-identity" type="float" value="@VALUE@" min="80" max="100" label="Minimum IDY% considered as proper alignment" help="Alignments with IDY% worse than this value will be filtered. Note that all alignments with IDY% less than 80.0% will be filtered regardless of this threshold. "/> + </xml> + <xml name="custom"> + <param name="custom" type="select" label="Use customized names for the input files?" help="They will be used in reports, plots and logs"> + <option value="true">Yes, specify custom names</option> + <option value="false" selected="true">No, use dataset names</option> + </param> + </xml> + <xml name="labelled_input"> + <param name="input" type="data" format="fasta" label="Contigs/scaffolds file"/> + <param argument="--labels" type="text" value="" label="Name"/> + </xml> + <xml name="reads_option"> + <param name="reads_option" type="select" label="Reads options" help="Currently, the supported read types are Illumina unpaired, paired-end and mate-pair reads, PacBio SMRT, and Oxford Nanopore long reads."> + <option value="disabled">Disabled</option> + <option value="single">Illumina single-end reads</option> + <option value="paired">Illumina paired-end reads</option> + <option value="paired_collection">Illumina paired-end reads in paired collection</option> + <option value="paired_interlaced">Illumina interlaced paired-end reads</option> + <option value="mate_paired">Illumina mate-pair reads</option> + <option value="pacbio">Pacbio SMRT reads</option> + <option value="nanopore">Nanopore reads</option> + </param> </xml> </macros> |
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| diff -r 3061c8b029e5 -r 72472698a2df quast.xml --- a/quast.xml Fri Aug 05 15:21:27 2022 +0000 +++ b/quast.xml Thu Mar 02 10:38:54 2023 +0000 |
| [ |
| b"@@ -10,19 +10,31 @@\n #import re\n #import os\n \n-#if str($in.custom) == 'false'\n- #set $labels = ','.join( [re.sub('[^\\w\\-_]', '_', str($x.element_identifier)) for $x in $in.inputs])\n+#if str($mode.in.custom) == 'false'\n+ #if $mode.mode == 'individual'\n+ #set $labels = re.sub('[^\\w\\-_]', '_', str($mode.in.inputs.element_identifier))\n+ #else\n+ #set $labels = ','.join( [re.sub('[^\\w\\-_]', '_', str($x.element_identifier)) for $x in $mode.in.inputs])\n+ #end if\n echo $labels &&\n #else\n- #set $labels = []\n- #for $x in $in.inputs\n- #if str($x.labels) != ''\n- #silent $labels.append(re.sub('[^\\w\\-_]', '_', str($x.labels)))\n+ #if $mode.mode == 'individual'\n+ #if str($mode.in.labels) != ''\n+ #set $labels = re.sub('[^\\w\\-_]', '_', str($mode.in.labels))\n #else\n- #silent $labels.append(re.sub('[^\\w\\-_]', '_', str($x.input.element_identifier)))\n+ #set $labels = re.sub('[^\\w\\-_]', '_', str($mode.in.input.element_identifier))\n #end if\n- #end for\n- #set $labels = ','.join($labels)\n+ #else\n+ #set $labels = []\n+ #for $x in $mode.in.inputs\n+ #if str($x.labels) != ''\n+ #silent $labels.append(re.sub('[^\\w\\-_]', '_', str($x.labels)))\n+ #else\n+ #silent $labels.append(re.sub('[^\\w\\-_]', '_', str($x.input.element_identifier)))\n+ #end if\n+ #end for\n+ #set $labels = ','.join($labels)\n+ #end if\n #end if\n \n #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list'\n@@ -32,19 +44,34 @@\n #end for\n #end if\n \n-#if $reads.reads_option == 'paired'\n- #for $read in $reads.input_1\n- #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($read.element_identifier))\n+#if $mode.reads.reads_option == 'paired'\n+ #if $mode.mode == 'individual'\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($mode.reads.input_1.element_identifier))\n+ln -s '$mode.reads.input_1' 'pe1-${identifier}.${mode.reads.input_1.ext}' &&\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($mode.reads.input_2.element_identifier))\n+ln -s '$mode.reads.input_2' 'pe2-${identifier}.${mode.reads.input_2.ext}' &&\n+ #else\n+ #for $read in $mode.reads.input_1\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($read.element_identifier))\n ln -s '$read' 'pe1-${identifier}.${read.ext}' &&\n- #end for\n- #for $read in $reads.input_2\n- #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($read.element_identifier))\n+ #end for\n+ #for $read in $mode.reads.input_2\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($read.element_identifier))\n ln -s '$read' 'pe2-${identifier}.${read.ext}' &&\n- #end for\n-#else if $reads.reads_option == 'paired_collection'\n- #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($reads.input_1.element_identifier))\n-ln -s '$reads.input_1.forward' 'pe1-${identifier}.${reads.input_1.forward.ext}' &&\n-ln -s '$reads.input_1.reverse' 'pe2-${identifier}.${reads.input_1.reverse.ext}' &&\n+ #end for\n+ #end if\n+#else if $mode.reads.reads_option == 'paired_collection'\n+ #if $mode.mode == 'individual'\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($mode.reads.input_1.element_identifier))\n+ln -s '$mode.reads.input_1.forward' 'pe1-${identifier}.${mode.reads.input_1.forward.ext}' &&\n+ln -s '$mode.reads.input_1.reverse' 'pe2-${identifier}.${mode.reads.input_1.reverse.ext}' &&\n+ #else\n+ #for $read in $mode.reads.input_1\n+ #set $identifier = re.sub('[^\\s\\w\\-\\\\.]', '_', str($read.element_identifier))\n+ln -s '$read.forward' 'pe1-${identifier}.${read.forward.ext}' &&\n+ln -s '$read.reverse' 'pe2-${identifier}.${read.reverse.ext}' &&\n+ #end for\n+ #end if\n #end if\n \n #if $assembly.type == 'genome'\n@@ -53,44 +80,79 @@\n metaquast\n #end if\n \n-#if $reads.reads_option == 'single'\n- #for $read in $reads.input_1\n+#if $mode.reads.reads_option == 'single'\n+ "..b'tom" value="true"/>\n- <repeat name="inputs">\n+ <conditional name="mode">\n+ <param name="mode" value="individual"/>\n+ <conditional name="in">\n+ <param name="custom" value="true"/>\n <param name="input" value="contigs1.fna"/>\n <param name="labels" value="contig1"/>\n- </repeat>\n- </conditional>\n- <conditional name="reads">\n- <param name="reads_option" value="paired_collection"/>\n- <param name="input_1">\n- <collection type="paired">\n- <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n- <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n- </collection>\n- </param>\n+ </conditional>\n+ <conditional name="reads">\n+ <param name="reads_option" value="paired_collection"/>\n+ <param name="input_1">\n+ <collection type="paired">\n+ <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </param>\n+ </conditional>\n </conditional>\n <conditional name="assembly">\n <param name="type" value="genome"/>\n@@ -909,6 +1040,50 @@\n </assert_contents>\n </output>\n </test>\n+ <!-- Test 13: Test co-assembly with paired-collection fastq.gz inputs -->\n+ <test expect_num_outputs="1">\n+ <conditional name="mode">\n+ <param name="mode" value="co"/>\n+ <conditional name="in">\n+ <param name="custom" value="false"/>\n+ <param name="inputs" value="contigs1.fna,contigs2.fna"/>\n+ </conditional>\n+ <conditional name="reads">\n+ <param name="reads_option" value="paired_collection"/>\n+ <param name="input_1">\n+ <collection type="list:paired">\n+ <element name="s1">\n+ <collection type="paired">\n+ <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </element>\n+ <element name="s2">\n+ <collection type="paired">\n+ <element name="forward" value="reads1.fastq.gz" ftype="fastqsanger.gz"/>\n+ <element name="reverse" value="reads2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ </conditional>\n+ </conditional>\n+ <conditional name="assembly">\n+ <param name="type" value="genome"/>\n+ <conditional name="ref">\n+ <param name="use_ref" value="false"/>\n+ </conditional>\n+ </conditional>\n+ <param name="output_files" value="tabular"/>\n+ <output name="report_tabular" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="# contigs (>= 0 bp)"/>\n+ <has_text text="contigs1"/>\n+ <has_text text="# N\'s per 100 kbp"/>\n+ <has_n_lines n="22"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |