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annotate insertion_profile.xml @ 63:27e16a30667a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
author iuc
date Tue, 09 Apr 2024 11:24:55 +0000
parents 473382134e56
children
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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 <expand macro="bio_tools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <version_command><![CDATA[insertion_profile.py --version]]></version_command>
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12 <command><![CDATA[
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13 @BAM_SAM_INPUTS@
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14 insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <expand macro="bam_sam_param"/>
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19 <expand macro="mapq_param"/>
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20 <expand macro="layout_param"/>
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21 <expand macro="rscript_output_param"/>
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22 </inputs>
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23 <outputs>
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24 <expand macro="pdf_output_data" filename="output.insertion_profile.pdf"/>
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25 <expand macro="xls_output_data" filename="output.insertion_profile.xls"/>
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26 <expand macro="rscript_output_data" filename="output.insertion_profile.r"/>
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27 </outputs>
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28 <tests>
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29 <test expect_num_outputs="3">
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30 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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31 <param name="rscript_output" value="true"/>
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32 <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size"/>
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33 <output name="outputxls" file="output.insertion_profile.xls" ftype="tabular"/>
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34 <output name="outputr" file="output.insertion_profile_r"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 insertion_profile.py
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39 ++++++++++++++++++++
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41 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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42 use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.
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44 Inputs
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45 ++++++
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47 Input BAM/SAM file
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48 Alignment file in BAM/SAM format.
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50 Minimum mapping quality
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51 Minimum mapping quality for an alignment to be considered as "uniquely
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52 mapped". default=30
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54 Sequencing layout
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55 Denotes whether the sequecing was single-end (SE) or paired-end (PE).
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57 Sample Output
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58 ++++++++++++++
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60 Read-1 insertion profile:
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62 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
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63 :height: 600 px
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64 :width: 600 px
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65 :scale: 80 %
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67 Read-2 insertion profile:
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69 .. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.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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74 @ABOUT@
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76 ]]>
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77 </help>
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78 <expand macro="citations"/>
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79 </tool>