Mercurial > repos > nilesh > rseqc

annotate inner_distance.xml @ 61:5968573462fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:23:05 +0000
parents 1421603cc95b
children 27e16a30667a
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60
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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1 <tool id="rseqc_inner_distance" name="Inner Distance" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>calculate the inner distance (or insert size) between two paired RNA reads</description>
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3 <macros>
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4 <import>rseqc_macros.xml</import>
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5 </macros>
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6
61
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
iuc
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7 <expand macro="bio_tools"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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8
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9 <expand macro="requirements" />
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10
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11 <expand macro="stdio" />
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12
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13 <version_command><![CDATA[inner_distance.py --version]]></version_command>
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15 <command><![CDATA[
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1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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16 @BAM_SAM_INPUTS@
1421603cc95b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 1dfe55ca83685cadb0ce8f6ebbd8c13232376d1d
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17 inner_distance.py -i 'input.${extension}' -o output -r '${refgene}'
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18 --sample-size ${sample_size}
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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19 --lower-bound ${lowerBound}
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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20 --upper-bound ${upperBound}
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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21 --step ${step}
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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22 --mapq ${mapq}
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23 ]]>
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24 </command>
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25
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26 <inputs>
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27 <expand macro="bam_sam_param" />
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28 <expand macro="refgene_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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29 <expand macro="sample_size_param" />
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30 <param name="lowerBound" type="integer" value="-250" label="Lower bound (bp, default=-250)" help="Used for plotting histogram (--lower-bound)"/>
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31 <param name="upperBound" type="integer" value="250" label="Upper bound (bp, default=250)" help="Used for plotting histogram (--upper-bound)"/>
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32 <param name="step" type="integer" value="5" label="Step size of histogram (bp, default=5)" help="(--step)"/>
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33 <expand macro="mapq_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 <expand macro="rscript_output_param" />
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35 </inputs>
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36
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37 <outputs>
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38 <expand macro="pdf_output_data" filename="output.inner_distance_plot.pdf" label="${tool.name} on ${on_string}: plot (PDF)"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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39 <data format="txt" name="outputtxt" from_work_dir="output.inner_distance.txt" label="${tool.name} on ${on_string}: TXT"/>
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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40 <data format="txt" name="outputfreqtxt" from_work_dir="output.inner_distance_freq.txt" label="${tool.name} on ${on_string}: frequency (TXT)" />
5968573462fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
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41 <expand macro="rscript_output_data" filename="output.inner_distance_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
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42 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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47 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed" ftype="bed12"/>
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48 <param name="rscript_output" value="true" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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49 <output name="outputtxt" file="output.inner_distance.txt" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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50 <output name="outputfreqtxt" file="output.inner_distance_freq.txt" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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51 <output name="outputpdf" file="output.inner_distance_plot.pdf" compare="sim_size"/>
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52 <output name="outputr" file="output.inner_distance_plot_r" />
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53 </test>
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54 </tests>
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56 <help><![CDATA[
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57 inner_distance.py
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58 +++++++++++++++++
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59
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60 This module is used to calculate the inner distance (or insert size) between two paired RNA
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61 reads. The distance is the mRNA length between two paired fragments. We first determine the
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62 genomic (DNA) size between two paired reads: D_size = read2_start - read1_end, then
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63
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64 * if two paired reads map to the same exon: inner distance = D_size
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65 * if two paired reads map to different exons:inner distance = D_size - intron_size
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66 * if two paired reads map non-exonic region (such as intron and intergenic region): inner distance = D_size
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67 * The inner_distance might be a negative value if two fragments were overlapped.
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68
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69 NOTE: Not all read pairs were used to estimate the inner distance distribution. Those low
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70 quality, PCR duplication, multiple mapped reads were skipped.
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71
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72 Inputs
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73 ++++++++++++++
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74
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75 Input BAM/SAM file
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76 Alignment file in BAM/SAM format.
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77
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78 Reference gene model
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79 Gene model in BED format.
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80
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81 Estimated Upper/Lower Bounds (defaults=250 and -250)
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82 Estimated upper/lower bounds of inner distance (bp).
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83
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84 Step size (default=5)
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85 Step size of histogram
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87
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88 Output
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89 ++++++++++++++
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90
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91 1. output.inner_distance.txt:
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92 - first column is read ID
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93 - second column is inner distance. Could be negative value if PE reads were overlapped or mapping error (e.g. Read1_start &lt; Read2_start, while Read1_end >> Read2_end due to spliced mapping of read1)
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94 - third column indicates how paired reads were mapped: PE_within_same_exon, PE_within_diff_exon,PE_reads_overlap
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95 2. output..inner_distance_freq.txt:
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96 - inner distance starts
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97 - inner distance ends
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98 - number of read pairs
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99 - note the first 2 columns are left side half open interval
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100 3. output.inner_distance_plot.r: R script to generate histogram
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101 4. output.inner_distance_plot.pdf: histogram plot
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102
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103 .. image:: $PATH_TO_IMAGES/inner_distance.png
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104 :height: 600 px
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105 :width: 600 px
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106 :scale: 80 %
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107
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108 @ABOUT@
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109
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110 ]]>
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111 </help>
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6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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113 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
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114
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
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115 </tool>