| Previous changeset 0:d27a4ed006ee (2022-01-28) Next changeset 2:a4441f35f17b (2022-08-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metabat2/ commit f239f2bb562330c955c19c328935793d6f1f2aa7 |
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modified:
jgi_summarize_bam_contig_depths.xml macros.xml |
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| diff -r d27a4ed006ee -r 1592150e38d2 jgi_summarize_bam_contig_depths.xml --- a/jgi_summarize_bam_contig_depths.xml Fri Jan 28 12:21:33 2022 +0000 +++ b/jgi_summarize_bam_contig_depths.xml Fri Jul 29 12:37:53 2022 +0000 |
| [ |
| b'@@ -2,81 +2,127 @@\n <description>for MetaBAT2</description>\n <macros>\n <import>macros.xml</import>\n+ <xml name="use_reference">\n+ <param name="use_reference" type="select" label="Select a reference genome?">\n+ <option value="no" selected="true">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ </xml>\n+ <xml name="reference_source">\n+ <param name="reference_source" type="select" label="Choose the source for the reference genome">\n+ <option value="cached" selected="true">locally cached</option>\n+ <option value="history">from history</option>\n+ </param>\n+ </xml>\n+ <xml name="referenceFasta">\n+ <param argument="--referenceFasta" type="data" format="fasta,fasta.gz" label="Using reference genome" help="Must be the reference used to map the input bam files"/>\n+ </xml>\n+ <xml name="gcWindow">\n+ <param argument="--gcWindow" type="integer" value ="100" label="Sliding window size for GC calculations"/>\n+ </xml>\n </macros>\n <expand macro="requirements"/>\n <command detect_errors="exit_code"><![CDATA[\n-jgi_summarize_bam_contig_depths \n---outputDepth \'$outputDepth\'\n---percentIdentity $advanced.percentIdentity\n-#if str($advanced.output_paired_contigs) == \'yes\':\n+jgi_summarize_bam_contig_depths\n+ --outputDepth \'$outputDepth\'\n+ --percentIdentity $advanced.percentIdentity\n+#if $advanced.output_paired_contigs\n --pairedContigs \'$outputPairedContigs\'\n #end if\n-$advanced.noIntraDepthVariance\n-$advanced.showDepth\n---minMapQual $advanced.minMapQual\n---weightMapQual $advanced.weightMapQual\n-$advanced.includeEdgeBases\n---maxEdgeBases $advanced.maxEdgeBases\n-#if str($advanced.use_reference_cond.use_reference) == \'yes\':\n- #if str($advanced.use_reference_cond.reference_cond.reference_source) == \'cached\'\n- --referenceFasta \'$advanced.use_reference_cond.reference_cond.referenceFasta.fields.path\'\n- #else:\n- --referenceFasta \'$advanced.use_reference_cond.reference_cond.referenceFasta\'\n+ $advanced.noIntraDepthVariance\n+ $advanced.showDepth\n+ --minMapQual $advanced.minMapQual\n+ --weightMapQual $advanced.weightMapQual\n+ $advanced.includeEdgeBases\n+ --maxEdgeBases $advanced.maxEdgeBases\n+#if str($mode.use_reference_cond.use_reference) == \'yes\'\n+ #if str($mode.use_reference_cond.reference_cond.reference_source) == \'cached\'\n+ --referenceFasta \'$mode.use_reference_cond.reference_cond.referenceFasta.fields.path\'\n+ #else\n+ --referenceFasta \'$mode.use_reference_cond.reference_cond.referenceFasta\'\n #end if\n --outputGC \'$outputGC\'\n- --gcWindow $advanced.use_reference_cond.gcWindow\n+ --gcWindow $mode.use_reference_cond.gcWindow\n --outputReadStats \'$outputReadStats\'\n --outputKmers \'$outputKmers\'\n #end if\n---shredLength $shredding.shredLength\n---shredDepth $shredding.shredDepth\n---minContigLength $shredding.minContigLength\n---minContigDepth $shredding.minContigDepth\n-#for bam_input in $bam_inputs:\n+ --shredLength $shredding.shredLength\n+ --shredDepth $shredding.shredDepth\n+ --minContigLength $shredding.minContigLength\n+ --minContigDepth $shredding.minContigDepth\n+#if $mode.type == \'individual\'\n+ \'$mode.bam_indiv_input\'\n+#else\n+ #for $bam_input in $mode.bam_co_inputs\n \'$bam_input\'\n-#end for\n+ #end for\n+#end if\n ]]></command>\n <inputs>\n- <param name="bam_inputs" type="data" format="bam" multiple="true" label="Sorted bam files"/>\n+ <conditional name="mode">\n+ <param name="type" type="select" label="Mode to process BAM files">\n+ <option value="individual">One by one</option>\n+ <option value="co">Together</option>\n+ </param>\n+ <when value="individual">\n+ <param name="bam_indiv_input" type="data" format="bam" label="Sorted bam files"/>\n+ <conditi'..b'fault settings -->\n <test expect_num_outputs="1">\n- <param name="bam_inputs" value="input1.bam,input1.bam" ftype="bam"/>\n+ <conditional name="mode">\n+ <param name="type" value="co"/>\n+ <param name="bam_co_inputs" value="input1.bam,input1.bam" ftype="bam"/>\n+ </conditional>\n <output name="outputDepth" file="jgi_output2.tabular" ftype="tabular" compare="contains"/>\n </test>\n <!-- Single input, output paired contigs, reference from history -->\n <test expect_num_outputs="5">\n- <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/>\n- <param name="output_paired_contigs" value="yes"/>\n- <param name="use_reference" value="yes"/>\n- <param name="reference_source" value="history"/>\n- <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/>\n+ <conditional name="mode">\n+ <param name="type" value="individual"/>\n+ <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>\n+ <conditional name="use_reference_cond">\n+ <param name="use_reference" value="yes"/>\n+ <conditional name="reference_cond">\n+ <param name="reference_source" value="history"/>\n+ <param name="referenceFasta" value="NC_002945v4.fasta" ftype="fasta"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <section name="advanced">\n+ <param name="output_paired_contigs" value="true"/>\n+ </section>\n <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>\n <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>\n <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>\n@@ -126,10 +187,19 @@\n </test>\n <!-- Single input, output paired contigs, cached reference -->\n <test expect_num_outputs="5">\n- <param name="bam_inputs" value="input2.bam" ftype="bam" dbkey="89"/>\n- <param name="output_paired_contigs" value="yes"/>\n- <param name="use_reference" value="yes"/>\n- <param name="reference_source" value="cached"/>\n+ <conditional name="mode">\n+ <param name="type" value="individual"/>\n+ <param name="bam_indiv_input" value="input2.bam" ftype="bam" dbkey="89"/>\n+ <conditional name="use_reference_cond">\n+ <param name="use_reference" value="yes"/>\n+ <conditional name="reference_cond">\n+ <param name="reference_source" value="cached"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <section name="advanced">\n+ <param name="output_paired_contigs" value="true"/>\n+ </section>\n <output name="outputDepth" file="jgi_output_depth1.tabular" ftype="tabular" compare="contains"/>\n <output name="outputPairedContigs" file="jgi_output_paired_contigs1.fasta" ftype="fasta"/>\n <output name="outputGC" file="jgi_output_gc1.tabular" ftype="tabular"/>\n@@ -137,7 +207,7 @@\n <output name="outputKmers" file="jgi_output_kmers1.tabular" ftype="tabular"/>\n </test>\n </tests>\n- <help>\n+ <help><![CDATA[\n **What it does**\n \n Calculates coverage depth for each sequence in one or more selected BAM files, producing a tabular file (for each input)\n@@ -172,7 +242,7 @@\n \n * **Select a reference genome** - optionally select the reference genome that was used to map the input bam file(s) and 3 additional outputs will be produced; gc coverage histogram, read statistics and perfect kmer counts.\n \n- </help>\n+ ]]></help>\n <expand macro="citations"/>\n </tool>\n \n' |
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| diff -r d27a4ed006ee -r 1592150e38d2 macros.xml --- a/macros.xml Fri Jan 28 12:21:33 2022 +0000 +++ b/macros.xml Fri Jul 29 12:37:53 2022 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.15</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements> |