Mercurial > repos > nilesh > rseqc

annotate insertion_profile.xml @ 14:b21f0167e197 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit ccb6f7edba5492f4750ef8a59c4f91eb67fdbbec
author iuc
date Wed, 22 Feb 2023 15:05:13 +0000
parents a7f9084572fe
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1 <tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 calculates the distribution of inserted nucleotides across reads
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4 </description>
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5 <macros>
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6 <import>rseqc_macros.xml</import>
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7 </macros>
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8
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9 <expand macro="bio_tools"/>
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10
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11 <expand macro="requirements" />
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13 <expand macro="stdio" />
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15 <version_command><![CDATA[insertion_profile.py --version]]></version_command>
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17 <command><![CDATA[
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18 @BAM_SAM_INPUTS@
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19 insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
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20 ]]>
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21 </command>
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23 <inputs>
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24 <expand macro="bam_sam_param" />
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25 <expand macro="mapq_param" />
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26 <expand macro="layout_param" />
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27 <expand macro="rscript_output_param" />
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28 </inputs>
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30 <outputs>
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31 <expand macro="pdf_output_data" filename="output.insertion_profile.pdf" />
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32 <expand macro="xls_output_data" filename="output.insertion_profile.xls" />
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33 <expand macro="rscript_output_data" filename="output.insertion_profile.r" />
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34 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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39 <param name="rscript_output" value="true" />
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40 <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size" />
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41 <output name="outputxls" file="output.insertion_profile.xls" ftype="tabular"/>
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42 <output name="outputr" file="output.insertion_profile_r" />
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43 </test>
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44 </tests>
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46 <help><![CDATA[
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47 insertion_profile.py
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48 ++++++++++++++++++++
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50 Calculate the distributions of inserted nucleotides across reads. Note that to
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51 use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.
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53 Inputs
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54 ++++++
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56 Input BAM/SAM file
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57 Alignment file in BAM/SAM format.
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59 Minimum mapping quality
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60 Minimum mapping quality for an alignment to be considered as "uniquely
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61 mapped". default=30
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63 Sequencing layout
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64 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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66 Sample Output
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67 ++++++++++++++
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69 Read-1 insertion profile:
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71 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
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72 :height: 600 px
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73 :width: 600 px
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74 :scale: 80 %
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76 Read-2 insertion profile:
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78 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.png
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79 :height: 600 px
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80 :width: 600 px
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81 :scale: 80 %
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83 @ABOUT@
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85 ]]>
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86 </help>
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88 <expand macro="citations" />
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90 </tool>