Mercurial > repos > nilesh > rseqc

annotate deletion_profile.xml @ 62:473382134e56 draft

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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 15:06:01 +0000
parents 5968573462fa
children 27e16a30667a
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1 <tool id="rseqc_deletion_profile" name="Deletion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
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2 <description>
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3 calculates the distributions of deleted 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[deletion_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 deletion_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
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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_param" />
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25 <expand macro="readlength_param" />
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26 <expand macro="readnum_param" />
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27 <expand macro="mapq_param" />
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28 <expand macro="rscript_output_param" />
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29 </inputs>
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31 <outputs>
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32 <expand macro="pdf_output_data" filename="output.deletion_profile.pdf" />
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33 <expand macro="xls_output_data" filename="output.deletion_profile.txt" />
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34 <expand macro="rscript_output_data" filename="output.deletion_profile.r" />
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35 </outputs>
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37 <tests>
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38 <test>
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39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
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40 <param name="read_align_length" value="101" />
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41 <param name="rscript_output" value="true" />
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42 <output name="outputpdf" file="output.deletion_profile.pdf" compare="sim_size" />
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43 <output name="outputxls" file="output.deletion_profile.txt" ftype="tabular"/>
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dbedfc5f5a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 247059e2527b66f1dbecf1e61496daef921040c3"
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44 <output name="outputr" file="output.deletion_profile_r" />
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45 </test>
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46 </tests>
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48 <help><![CDATA[
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49 deletion_profile.py
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50 +++++++++++++++++++
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52 Calculate the distributions of deleted nucleotides across reads.
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54 Inputs
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55 ++++++
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57 Input BAM/SAM file
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58 Alignment file in BAM/SAM format.
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60 Alignment length of read
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61 It is usually set to the orignial read length. For example, all these cigar
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62 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
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63 length is 101. [required]
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65 Number of aligned reads used
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66 Number of aligned reads with deletions used to calculate the deletion
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67 profile. default=1000000
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69 Minimum mapping quality
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70 Minimum mapping quality for an alignment to be considered as "uniquely
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71 mapped". default=30
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73 Sample Output
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74 ++++++++++++++
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76 .. image:: $PATH_TO_IMAGES/out.deletion_profile.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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81 @ABOUT@
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83 ]]>
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85 </help>
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87 <expand macro="citations" />
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89 </tool>