Mercurial > repos > nilesh > rseqc

annotate insertion_profile.xml @ 51:09846d5169fa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
author iuc
date Tue, 14 Mar 2017 10:23:21 -0400
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51
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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1 <tool id="rseqc_insertion_profile" name="Insertion Profile" version="@WRAPPER_VERSION@">
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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2 <description>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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3 calculates the distribution of inserted nucleotides across reads
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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4 </description>
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6 <macros>
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7 <import>rseqc_macros.xml</import>
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8 </macros>
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10 <expand macro="requirements" />
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12 <expand macro="stdio" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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14 <version_command><![CDATA[insertion_profile.py --version]]></version_command>
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16 <command><![CDATA[
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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17 insertion_profile.py -i '${input}' -o output -q ${mapq} -s "${layout}"
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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18 ]]>
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19 </command>
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21 <inputs>
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22 <expand macro="bam_param" />
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23 <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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24 <expand macro="layout_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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25 <expand macro="rscript_output_param" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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26 </inputs>
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28 <outputs>
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29 <expand macro="pdf_output_data" filename="output.insertion_profile.pdf" />
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30 <expand macro="xls_output_data" filename="output.insertion_profile.xls" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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31 <expand macro="rscript_output_data" filename="output.insertion_profile.r" />
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32 </outputs>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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34 <tests>
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35 <test>
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36 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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37 <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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38 <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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39 <output name="outputxls" file="output.insertion_profile.xls" />
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40 <output name="outputr" file="output.insertion_profile.r" />
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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41 </test>
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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42 </tests>
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44 <help><![CDATA[
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45 insertion_profile.py
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46 ++++++++++++++++++++
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09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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48 Calculate the distributions of inserted nucleotides across reads. Note that to
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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49 use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.
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51 Inputs
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52 ++++++
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54 Input BAM/SAM file
09846d5169fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 37fb1988971807c6a072e1afd98eeea02329ee83
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55 Alignment file in BAM/SAM format.
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56
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57 Minimum mapping quality
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58 Minimum mapping quality for an alignment to be considered as "uniquely
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59 mapped". default=30
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60
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61 Sequencing layout
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62 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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63
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64 Sample Output
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65 ++++++++++++++
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66
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67 Read-1 insertion profile:
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68
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69 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
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70 :height: 600 px
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71 :width: 600 px
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72 :scale: 80 %
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73
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74 Read-2 insertion profile:
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75
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76 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.png
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77 :height: 600 px
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78 :width: 600 px
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79 :scale: 80 %
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80
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81 @ABOUT@
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82
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83 ]]>
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84 </help>
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85
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86 <expand macro="citations" />
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87
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88 </tool>