| Previous changeset 1:00852209fd9f (2015-10-21) Next changeset 3:31782dbb7d85 (2016-07-09) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_size_histograms commit 89caea4594db1ae6d6bb9c651bc6019bb6dd3ce6 |
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modified:
size_histogram.xml tool_dependencies.xml |
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| diff -r 00852209fd9f -r a95419680ce4 size_histogram.xml --- a/size_histogram.xml Wed Oct 21 11:50:42 2015 -0400 +++ b/size_histogram.xml Thu Mar 10 11:00:00 2016 -0500 |
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| b'@@ -1,99 +1,99 @@\n-<tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.7">\n- <description>from sRbowtie aligment</description>\n- <requirements>\n+<tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.8">\n+ <description>from sRbowtie aligment</description>\n+ <requirements>\n <requirement type="package" version="0.12.7">bowtie</requirement>\n <requirement type="package" version="0.7.7">pysam</requirement>\n <requirement type="package" version="3.1.2">R</requirement>\n <requirement type="package" version="2.14">biocbasics</requirement>\n <requirement type="package" version="1.9">numpy</requirement>\n- </requirements>\n-<command interpreter="python">\n- size_histogram.py \n-\t #if $refGenomeSource.genomeSource == "history":\n- \t --reference_fasta ## sys.argv[2]\n- $refGenomeSource.ownFile ## index source\n- \t #else:\n- #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ \'bowtie_indexes\' ].get_fields() )[0][-1]\n-\t\t --reference_bowtie_index\n- $reference\n- \t #end if\n-\t\t --rcode\n-\t\t $plotCode\n-\t\t --output_size_distribution\n-\t\t $size_distribution_dataframe\n-\t\t --minquery\n-\t\t $minquery\n-\t\t --maxquery\n-\t\t $maxquery\n-\t\t --input\n-\t\t #for $i in $refGenomeSource.series\n- \t\t $i.input \n-\t\t #end for\n-\t\t --ext\n-\t\t #for $i in $refGenomeSource.series\n- \t\t $i.input.ext \n-\t\t #end for\n-\t\t --label\n-\t\t #for $i in $refGenomeSource.series\n- \t\t "$i.input.name" \n-\t\t #end for\n-\t\t --normalization_factor\n-\t\t #for $i in $refGenomeSource.series\n- \t\t $i.norm\n-\t\t #end for\n-\t\t #if $gff:\n-\t\t --gff\n- $gff\n- #end if\n- #if $global.value == \'yes\':\n- --global_size\n- #end if\n- #if $collapsestrands.value == \'yes\':\n- --collapse\n- #end if\n+ </requirements>\n+ <command interpreter="python">\n+ size_histogram.py\n+ #if $refGenomeSource.genomeSource == "history":\n+ --reference_fasta ## sys.argv[2]\n+ $refGenomeSource.ownFile ## index source\n+ #else:\n+ #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ \'bowtie_indexes\' ].get_fields() )[0][-1]\n+ --reference_bowtie_index\n+ $reference\n+ #end if\n+ --rcode\n+ $plotCode\n+ --output_size_distribution\n+ $size_distribution_dataframe\n+ --minquery\n+ $minquery\n+ --maxquery\n+ $maxquery\n+ --input\n+ #for $i in $refGenomeSource.series\n+ $i.input\n+ #end for\n+ --ext\n+ #for $i in $refGenomeSource.series\n+ $i.input.ext\n+ #end for\n+ --label\n+ #for $i in $refGenomeSource.series\n+ "$i.input.name"\n+ #end for\n+ --normalization_factor\n+ #for $i in $refGenomeSource.series\n+ $i.norm\n+ #end for\n+ #if $gff:\n+ --gff $gff\n+ #end if\n+ #if $global.value == \'yes\':\n+ --global_size\n+ #end if\n+ #if $collapsestrands.value == \'yes\':\n+ --collapse\n+ #end if\n \n-</command>\n- <inputs>\n- <conditional name="refGenomeSource">\n- <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">\n- <option value="indexed">Use a built-in index</option>\n- <option value="history">Use one from the history</option>\n- </param>\n- <when value="indexed">\n-\t <repeat name="series" title="Add alignment files">\n-\t <param'..b'ber=4, rot=90, relation="same"), cex=1),\n+ xlab = "readsize in nucleotides",\n+ ylab = "${ylabel}",\n+ ylim = ylim,\n+ main="${title}" , as.table=TRUE, newpage = T,\n+ aspect=0.5,\n+ strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")\n+ )\n+ bc\n+ }\n+\n devname=dev.off()\n \n </configfile>\n </configfiles>\n-\n- <outputs>\n- <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>\n- <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>\n- </outputs>\n+ <outputs>\n+ <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>\n+ <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>\n+ </outputs>\n <help>\n \n **What it does**\n \n-Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes, \n-where by default for each "chromosome" a histogram of read sizes is drawn. \n+Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes,\n+where by default for each "chromosome" a histogram of read sizes is drawn.\n Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).\n \n \n@@ -209,32 +231,32 @@\n \n ----\n \n-.. image:: static/images/size_histogram.png \n- :height: 800 \n+.. image:: static/images/size_histogram.png\n+ :height: 800\n :width: 500\n \n </help>\n- <tests>\n- <test>\n- <param name="genomeSource" value="history" />\n- <param name="ownFile" value="transposons.fasta" ftype="fasta" />\n- <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>\n- <param name="series_0|norm" value="1" />\n- <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>\n- <param name="series_1|norm" value="1" />\n- <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>\n- <param name="series_2|norm" value="1" />\n- <param name="global" value="no" />\n- <param name="collapsestrands" value="no" />\n- <param name="minquery" value="18"/>\n- <param name="maxquery" value="30"/>\n- <param name="title" value="Size distribution"/>\n- <param name="xlabel" value="Size in nucleotides"/>\n- <param name="ylabel" value="Number of reads"/>\n- <param name="rows_per_page" value="10"/>\n- <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />\n- <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />\n- </test>\n- </tests>\n+ <tests>\n+ <test>\n+ <param name="genomeSource" value="history" />\n+ <param name="ownFile" value="transposons.fasta" ftype="fasta" />\n+ <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>\n+ <param name="series_0|norm" value="1" />\n+ <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>\n+ <param name="series_1|norm" value="1" />\n+ <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>\n+ <param name="series_2|norm" value="1" />\n+ <param name="global" value="no" />\n+ <param name="collapsestrands" value="no" />\n+ <param name="minquery" value="18"/>\n+ <param name="maxquery" value="30"/>\n+ <param name="title" value="Size distribution"/>\n+ <param name="xlabel" value="Size in nucleotides"/>\n+ <param name="ylabel" value="Number of reads"/>\n+ <param name="rows_per_page" value="10"/>\n+ <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />\n+ <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />\n+ </test>\n+ </tests>\n </tool>\n \n' |
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| diff -r 00852209fd9f -r a95419680ce4 tool_dependencies.xml --- a/tool_dependencies.xml Wed Oct 21 11:50:42 2015 -0400 +++ b/tool_dependencies.xml Thu Mar 10 11:00:00 2016 -0500 |
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| @@ -7,10 +7,10 @@ <repository changeset_revision="0a5141bdf9d0" name="package_pysam_0_7_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> - <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c8f7a7d73466" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> - <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="c987143177d4" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="biocbasics" version="2.14"> <repository changeset_revision="f0ef1a7b157e" name="package_biocbasics_2_14" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" /> |