Mercurial > repos > artbio > small_rna_maps
comparison small_rna_maps.xml @ 2:507383cce5a8 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
| author | artbio |
|---|---|
| date | Mon, 14 Aug 2017 05:52:34 -0400 |
| parents | 40972a8dfab9 |
| children | ed8b0142538d |
comparison
equal
deleted
inserted
replaced
| 1:40972a8dfab9 | 2:507383cce5a8 |
|---|---|
| 1 <tool id="small_rna_maps" name="small_rna_maps" version="0.9.1"> | 1 <tool id="small_rna_maps" name="small_rna_maps" version="1.0.0"> |
| 2 <description></description> | 2 <description></description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> | 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> |
| 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> | 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> |
| 6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> | 6 <requirement type="package" version="1.3.2=r3.3.1_0">r-optparse</requirement> |
| 9 </requirements> | 9 </requirements> |
| 10 <stdio> | 10 <stdio> |
| 11 <exit_code range="1:" level="fatal" description="Tool exception" /> | 11 <exit_code range="1:" level="fatal" description="Tool exception" /> |
| 12 </stdio> | 12 </stdio> |
| 13 <command detect_errors="exit_code"><![CDATA[ | 13 <command detect_errors="exit_code"><![CDATA[ |
| 14 #for $file in $input | 14 #for $file in $inputs |
| 15 samtools index '$file' && | 15 samtools index '$file' && |
| 16 #end for | 16 #end for |
| 17 python '$__tool_directory__'/small_rna_maps.py | 17 python '$__tool_directory__'/small_rna_maps.py |
| 18 --input | 18 --inputs |
| 19 #for $file in $input | 19 #for $file in $inputs |
| 20 '$file' | 20 '$file' |
| 21 #end for | 21 #end for |
| 22 --sample_name | 22 --sample_names |
| 23 #for $sample in $input | 23 #for $sample in $inputs |
| 24 '$sample.name' | 24 '$sample.name' |
| 25 #end for | 25 #end for |
| 26 #if $extra_plot == 'Sizes': | 26 --plot_methods Counts $extra_plot |
| 27 --sizes '$output_sizes' | 27 --outputs $output_tab $extra_output_tab && |
| 28 #end if | 28 Rscript '$__tool_directory__'/small_rna_maps.r |
| 29 --output '$output_tab' && | 29 --first_dataframe '$output_tab' |
| 30 Rscript '$__tool_directory__'/small_rna_maps.r --output_tab '$output_tab' | 30 --extra_dataframe '$extra_output_tab' |
| 31 --output_pdf '$output_pdf' | 31 --extra_plot_method '$extra_plot' |
| 32 #if $extra_plot != 'Sizes': | 32 --output_pdf '$output_pdf' |
| 33 --extra_plot '$extra_plot' | |
| 34 #else | |
| 35 --sizes $output_sizes | |
| 36 #end if | |
| 37 ]]></command> | 33 ]]></command> |
| 38 <inputs> | 34 <inputs> |
| 39 <param name="input" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> | 35 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> |
| 40 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map"> | 36 <param name="extra_plot" type="select" label="select the type of extra plot in addition to read map"> |
| 41 <option value="Coverage">Coverage</option> | 37 <option value="Coverage">Coverage</option> |
| 42 <option value="Mean">Mean Sizes</option> | 38 <option value="Mean">Mean Sizes</option> |
| 43 <option value="Median">Median Sizes</option> | 39 <option value="Median">Median Sizes</option> |
| 44 <option value="Sizes">Size Distributions</option> | 40 <option value="Size">Size Distributions</option> |
| 45 </param> | 41 </param> |
| 46 </inputs> | 42 </inputs> |
| 47 | 43 |
| 48 <outputs> | 44 <outputs> |
| 49 <data format="tabular" name="output_tab" label="Map dataframe" /> | 45 <data format="tabular" name="output_tab" label="Read Count dataframe" /> |
| 50 <data format="tabular" name="output_sizes" label="Size dataframe" > | 46 <data format="tabular" name="extra_output_tab" label="$extra_plot dataframe" /> |
| 51 <filter>extra_plot == "Sizes"</filter> | |
| 52 </data> | |
| 53 <data format="pdf" name="output_pdf" label="PDF file" /> | 47 <data format="pdf" name="output_pdf" label="PDF file" /> |
| 54 | 48 |
| 55 </outputs> | 49 </outputs> |
| 56 | 50 |
| 57 <tests> | 51 <tests> |
| 58 <test> | 52 <test> |
| 59 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> | 53 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
| 60 <param name="extra_plot" value="Mean" /> | 54 <param name="extra_plot" value="Mean" /> |
| 61 <output file="output.tab" name="output_tab" /> | 55 <output file="readmap.tab" name="output_tab" /> |
| 56 <output file="mean.tab" name="extra_output_tab" /> | |
| 62 <output file="mean.pdf" name="output_pdf" /> | 57 <output file="mean.pdf" name="output_pdf" /> |
| 63 </test> | 58 </test> |
| 64 <test> | 59 <test> |
| 65 <param name="input" value="input1.bam,input1.bam" ftype="bam"/> | 60 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> |
| 66 <param name="extra_plot" value="Mean" /> | 61 <param name="extra_plot" value="Mean" /> |
| 67 <output file="doubled.tab" name="output_tab" /> | 62 <output file="doubled_readmap.tab" name="output_tab" /> |
| 63 <output file="double_mean.tab" name="extra_output_tab" /> | |
| 68 <output file="doubled_mean.pdf" name="output_pdf" /> | 64 <output file="doubled_mean.pdf" name="output_pdf" /> |
| 69 </test> | 65 </test> |
| 70 <test> | 66 <test> |
| 71 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> | 67 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
| 72 <param name="extra_plot" value="Median" /> | 68 <param name="extra_plot" value="Median" /> |
| 73 <output file="output.tab" name="output_tab" /> | 69 <output file="readmap.tab" name="output_tab" /> |
| 70 <output file="median.tab" name="extra_output_tab" /> | |
| 74 <output file="median.pdf" name="output_pdf" /> | 71 <output file="median.pdf" name="output_pdf" /> |
| 75 </test> | 72 </test> |
| 76 <test> | 73 <test> |
| 77 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> | 74 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
| 78 <param name="extra_plot" value="Coverage" /> | 75 <param name="extra_plot" value="Coverage" /> |
| 79 <output file="output.tab" name="output_tab" /> | 76 <output file="readmap.tab" name="output_tab" /> |
| 77 <output file="coverage.tab" name="extra_output_tab" /> | |
| 80 <output file="coverage.pdf" name="output_pdf" /> | 78 <output file="coverage.pdf" name="output_pdf" /> |
| 81 </test> | 79 </test> |
| 82 <test> | 80 <test> |
| 83 <param name="input" value="input1.bam,input2.bam" ftype="bam"/> | 81 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> |
| 84 <param name="extra_plot" value="Sizes" /> | 82 <param name="extra_plot" value="Size" /> |
| 85 <output file="output.tab" name="output_tab" /> | 83 <output file="readmap.tab" name="output_tab" /> |
| 86 <output file="sizes.tab" name="output_sizes" /> | 84 <output file="size.tab" name="extra_output_tab" /> |
| 87 <output file="sizes.pdf" name="output_pdf" /> | 85 <output file="sizes.pdf" name="output_pdf" /> |
| 88 </test> | 86 </test> |
| 89 </tests> | 87 </tests> |
| 90 | 88 |
| 91 | 89 |
| 97 | 95 |
| 98 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted. | 96 In addition to the read counts (lower graphs), median size, mean size and coverage depth of reads(lower graphs) mapping at a given position are plotted. |
| 99 | 97 |
| 100 **Inputs** | 98 **Inputs** |
| 101 | 99 |
| 102 bam alignment files that *must* be | 100 bam alignment files that must be |
| 103 | 101 |
| 104 - single-read | 102 - single-read |
| 105 - sorted | 103 - sorted |
| 106 - mapping to the same reference | 104 - mapping to the same reference |
| 107 | 105 |