| Previous changeset 2:acd337269171 (2019-06-20) Next changeset 4:edbb6c5028f5 (2020-01-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit 6afb87d2f226ac2fb61255b89dd9c36940b482c9 |
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modified:
nanoplot.xml |
| b |
| diff -r acd337269171 -r 645159bcee2d nanoplot.xml --- a/nanoplot.xml Thu Jun 20 10:18:48 2019 -0400 +++ b/nanoplot.xml Fri Jun 21 19:13:55 2019 -0400 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy0">\n+<tool id="nanoplot" name="NanoPlot" version="@TOOL_VERSION@+galaxy1">\n <description>Plotting suite for Oxford Nanopore sequencing data and alignments</description>\n <macros>\n <token name="@TOOL_VERSION@">1.25.0</token>\n@@ -7,123 +7,139 @@\n <requirement type="package" version="@TOOL_VERSION@">nanoplot</requirement>\n </requirements>\n <version_command>NanoPlot --version</version_command>\n- <command detect_errors="exit_code">\n- <![CDATA[\n+ <command detect_errors="exit_code"><![CDATA[\n+#set $myfiles = $mode.reads.files\n \n- #set reads_temp = []\n- #for $i, $f in enumerate($reads.files)\n+#set reads_temp = []\n+#if $mode.choice == \'combined\':\n+ #for $i, $f in enumerate($myfiles)\n+ #if $f.ext == "fastqsanger":\n+ #set $extension = \'fastq\'\n+ #else\n #set $extension = $f.ext\n- #if $extension == \'fastqsanger\'\n- #set $extension = \'fastq\'\n- #end if\n- ln -s \'$f\' \'./read_${i}.$extension\' &&\n- $reads_temp.append("read_" + str($i) + "." + str($extension))\n- #end for\n-\n- NanoPlot\n- --threads \\${GALAXY_SLOTS:-4}\n- --$reads.type ${\' \'.join($reads_temp)}\n+ #end if\n+ ln -s \'$f\' \'./read_${i}.$extension\' &&\n+ $reads_temp.append("read_" + str($i) + "." + str($extension))\n+ #end for\n+#else\n+ #if $myfiles.ext == "fastqsanger":\n+ #set $extension = \'fastq\'\n+ #else\n+ #set $extension = $myfiles.ext\n+ #end if\n+ ln -s \'$mode.reads.files\' \'./read.$extension\' &&\n+ $reads_temp.append("read." + str($extension))\n+#end if\n \n- #if $filter.maxlength\n- --maxlength $filter.maxlength\n- #end if\n- #if $filter.minlength\n- --minlength $filter.minlength\n- #end if\n- #if $filter.downsample\n- --downsample $filter.downsample\n- #end if\n- #if $filter.minqual\n- --minqual $filter.minqual\n- #end if\n- #if $filter.readtype\n- --readtype $filter.readtype\n- #end if\n- #if $customization.color\n- --color $customization.color\n- #end if\n- #if $customization.format\n- --format $customization.format\n- #end if\n- #if $customization.plots\n- --plots ${str($customization.plots).replace(\',\', \' \')}\n- #end if\n- $filter.drop_outliers\n- $filter.loglength\n- $filter.percentqual\n- $filter.alength\n- $filter.barcoded\n- $customization.noN50\n- $customization.N50\n- -o \'.\'\n- ]]>\n- </command>\n+NanoPlot\n+ --threads \\${GALAXY_SLOTS:-4}\n+ --$mode.reads.type ${\' \'.join($reads_temp)}\n+ #if $filter.maxlength\n+ --maxlength $filter.maxlength\n+ #end if\n+ #if $filter.minlength\n+ --minlength $filter.minlength\n+ #end if\n+ #if $filter.downsample\n+ --downsample $filter.downsample\n+ #end if\n+ #if $filter.minqual\n+ --minqual $filter.minqual\n+ #end if\n+ #if $filter.readtype\n+ --readtype $filter.readtype\n+ #end if\n+ #if $customization.color\n+ --color $customization.color\n+ #end if\n+ #if $customization.format\n+ --format $customization.format\n+ #end if\n+ #if $customization.plots\n+ --plots ${str($customization.plots).replace(\',\', \' \')}\n+ #end if\n+ $filter.drop_outliers\n+ $filter.loglength\n+ $filter.percentqual\n+ $filter.alength\n+ $filter.barcoded\n+ $customization.noN50\n+ $customization.N50\n+ -o \'.\'\n+ ]]></command>\n <inputs>\n- <conditional name="reads">\n- <param name="type" type="select" label="Type of the file(s) to work on">\n- <option value="fastq" selected="'..b' <when value="fasta">\n+ <param type="data" argument="--fasta" name="files" format="fasta,fasta.gz,vcf_bgzip" multiple="true"/>\n+ </when>\n+ <when value="fastq_rich">\n+ <param type="data" argument="--fastq_rich" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>\n+ </when>\n+ <when value="fastq_minimal">\n+ <param type="data" argument="--fastq_minimal" name="files" format="fastq,fastq.gz,fastq.bz2,vcf_bgzip" multiple="true"/>\n+ </when>\n+ <when value="summary">\n+ <param type="data" argument="--summary" name="files" format="txt,zip" multiple="true"/>\n+ </when>\n+ <when value="bam">\n+ <param type="data" argument="--bam" name="files" format="bam" multiple="true"/>\n+ </when>\n+ <when value="cram">\n+ <param type="data" argument="--cram" name="files" format="cram" multiple="true"/>\n+ </when>\n+ </conditional>\n </when>\n </conditional>\n <section\n@@ -399,9 +415,12 @@\n </outputs>\n <tests>\n <test>\n- <conditional name="reads">\n- <param name="type" value="fastq_rich"/>\n- <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>\n+ <conditional name="mode">\n+ <param name="choice" value="batch"/>\n+ <conditional name="reads">\n+ <param name="type" value="fastq_rich"/>\n+ <param name="files" value="reads.fastq.gz" ftype="fastq.gz"/>\n+ </conditional>\n </conditional>\n <section name="filter">\n <param name="downsample" value="800"/>\n@@ -415,9 +434,12 @@\n <output name="read_length" file="HistogramReadlength.png" ftype="png" compare="sim_size" delta="3000"/>\n </test>\n <test>\n- <conditional name="reads">\n- <param name="type" value="bam"/>\n- <param name="files" value="alignment.bam" ftype="bam"/>\n+ <conditional name="mode">\n+ <param name="choice" value="combined"/>\n+ <conditional name="reads">\n+ <param name="type" value="bam"/>\n+ <param name="files" value="alignment.bam" ftype="bam"/>\n+ </conditional>\n </conditional>\n <section name="filter">\n <param name="maxlength" value="2000"/>\n@@ -437,15 +459,18 @@\n <output name="read_length" file="bam-LogTransformed_HistogramReadlength.svg" ftype="svg" compare="sim_size"/>\n </test>\n <test><!-- test with multiple input files -->\n- <conditional name="reads">\n- <param name="type" value="fasta"/>\n- <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />\n+ <conditional name="mode">\n+ <param name="choice" value="combined"/>\n+ <conditional name="reads">\n+ <param name="type" value="fasta"/>\n+ <param name="files" ftype="fasta" value="reads1.fasta,reads2.fasta" />\n+ </conditional>\n </conditional>\n <output name="output_html" ftype="html">\n <assert_contents>\n <has_text text="html"/>\n <not_has_text text="Aligned read length vs Percent identity plot using dots"/> <!-- bam report specific -->\n- <has_text text="<td>9.0</td>"/> <!--check both files used 4+5 reads -->\n+ <has_text text="<td>9.0</td>"/> <!--check both files were used 4+5 reads -->\n </assert_contents>\n </output>\n </test>\n' |