Mercurial > repos > artbio > small_rna_maps
changeset 13:458a88317c22 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
| author | artbio |
|---|---|
| date | Tue, 10 Apr 2018 06:12:01 -0400 |
| parents | d33263e6e812 |
| children | cd75c72e1d75 |
| files | small_rna_maps.xml |
| diffstat | 1 files changed, 91 insertions(+), 54 deletions(-) [+] |
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--- a/small_rna_maps.xml Sat Apr 07 06:14:50 2018 -0400 +++ b/small_rna_maps.xml Tue Apr 10 06:12:01 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="2.5.0"> +<tool id="small_rna_maps" name="small_rna_maps" version="2.5.1"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement> @@ -13,33 +13,18 @@ <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ - #if $inputs_cond.normalize == "no": - #for $file in $inputs_cond.inputs - samtools index '$file'; - #end for - python '$__tool_directory__'/small_rna_maps.py - --inputs - #for $file in $inputs_cond.inputs - '$file' - #end for - --sample_names - #for $sample in $inputs_cond.inputs - '$sample.name' - #end for - #else if $inputs_cond.normalize == "yes": - #for $file in $inputs_cond.series + #for $file in $series samtools index '$file.inputs'; #end for python '$__tool_directory__'/small_rna_maps.py --inputs - #for $file in $inputs_cond.series + #for $file in $series '$file.inputs' #end for --sample_names - #for $sample in $inputs_cond.series + #for $sample in $series '$sample.inputs.name' #end for - #end if --minsize $minsize --maxsize $maxsize --cluster $cluster @@ -57,16 +42,12 @@ --first_dataframe '$output_tab' --extra_dataframe '$extra_output_tab' --normalization - #if $inputs_cond.normalize == "no": - '' - #else if $inputs_cond.normalize == "yes": - #set $norm = "" - #for $file in $inputs_cond.series - #set $norm += str($file.normalization)+' ' - #end for - #set $norm = $norm[:-1] - '$norm' - #end if + #set $norm = "" + #for $file in $series + #set $norm += str($file.normalization)+' ' + #end for + #set $norm = $norm[:-1] + '$norm' #if $ylimits_cond.ylimits == "no": --ymin '' --ymax '' #else: @@ -86,19 +67,12 @@ --output_pdf '$output_pdf' ]]></command> <inputs> - <conditional name="inputs_cond"> - <param name="normalize" type="boolean" label="Will there be normalization?" truevalue="yes" falsevalue="no" checked="false"/> - <when value="no"> - <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> - </when> - <when value="yes"> - <repeat name="series" title="Normalization factors" min="1"> - <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" /> - <param name="normalization" type="float" label="Enter size/normalization factors." - help="e.g. '0.75' '1.23'" value="1.0"/> - </repeat> - </when> - </conditional> + <repeat name="series" title="Input" min="1"> + <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false" + help="If 'multiple datasets' method is used, the same normalization factor will be applied to each dataset. Please refer to the help section for more information." /> + <param name="normalization" type="float" label="Enter a size/normalization factor." + help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/> + </repeat> <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" value="0" help="default value: 0" /> <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" @@ -166,7 +140,10 @@ <tests> <test> - <param name="inputs" value="input1.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -179,7 +156,10 @@ <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="5" /> @@ -189,7 +169,10 @@ <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="20" /> <param name="maxsize" value="30" /> <param name="cluster" value="0" /> @@ -199,7 +182,10 @@ <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -209,7 +195,10 @@ <output file="input1__single_plot_mean.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -219,7 +208,6 @@ <output file="input1_single_plot_median.pdf" name="output_pdf" /> </test> <test> - <param name="normalize" value="yes" /> <repeat name="series"> <param name="inputs" value="input1.bam" ftype="bam" /> <param name="normalization" value="1.0" /> @@ -237,7 +225,14 @@ <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input2.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -252,7 +247,30 @@ <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input_single_chr.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> @@ -262,26 +280,38 @@ <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input2.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> <param name="plots_options_selector" value="global" /> <param name="mergestrands" value="nomerge" /> <param name="first_plot" value="Size" /> - <param name="normalization" value="1 1" /> <output file="size.tab" name="output_tab" /> <output file="global_nomerge.pdf" name="output_pdf" /> </test> <test> - <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> + <repeat name="series"> + <param name="inputs" value="input1.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> + <repeat name="series"> + <param name="inputs" value="input2.bam" ftype="bam" /> + <param name="normalization" value="1.0" /> + </repeat> <param name="minsize" value="0" /> <param name="maxsize" value="10000" /> <param name="cluster" value="0" /> <param name="plots_options_selector" value="global" /> <param name="mergestrands" value="merge" /> <param name="first_plot" value="Size" /> - <param name="normalization" value="1 1" /> <output file="size.tab" name="output_tab" /> <output file="global_merge.pdf" name="output_pdf" /> </test> @@ -321,6 +351,13 @@ - sorted - mapped to the same reference +To plot 2 alignment files in the same PDF output the 'single dataset' method should be used. + +.. class:: warningmark + +If the 'multiple dataset' method is used the normalization factor will be applied to every file selected in the input list. +Additionally each file in the selected list will be plotted in a separate PDF file. + **Output** A pdf file generated by the R package lattice and one or two dataframes used to plot the data.