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annotate mismatch_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_mismatch_profile" name="Mismatch 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 mismatches 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[mismatch_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 mismatch_profile.py -i 'input.${extension}' -o output -l ${read_align_length} -n ${read_num} -q ${mapq}
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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_param"/>
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19 <expand macro="readlength_param"/>
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20 <expand macro="readnum_param"/>
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21 <expand macro="mapq_param"/>
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22 <expand macro="rscript_output_param"/>
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23 </inputs>
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24 <outputs>
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25 <expand macro="pdf_output_data" filename="output.mismatch_profile.pdf"/>
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26 <expand macro="xls_output_data" filename="output.mismatch_profile.xls"/>
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27 <expand macro="rscript_output_data" filename="output.mismatch_profile.r"/>
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28 </outputs>
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29 <tests>
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30 <test expect_num_outputs="3">
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31 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
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32 <param name="read_align_length" value="101"/>
27e16a30667a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit d7544582d5599c67a284faf9232cd2ccc4daa1de
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33 <param name="rscript_output" value="true"/>
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34 <output name="outputpdf" file="output.mismatch_profile.pdf" compare="sim_size"/>
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35 <output name="outputxls" file="output.mismatch_profile.xls" ftype="tabular"/>
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36 <output name="outputr" file="output.mismatch_profile_r"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 mismatch_profile.py
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41 +++++++++++++++++++
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43 Calculate the distribution of mismatches across reads.
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45 Note that the “MD” tag must exist in BAM file.
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47 Inputs
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48 ++++++
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50 Input BAM/SAM file
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51 Alignment file in BAM/SAM format.
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53 Alignment length of read
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54 It is usually set to the orignial read length. For example, all these cigar
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55 strings ("101M", "68M140N33M", "53M1D48M") suggest the read alignment
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56 length is 101. [required]
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58 Number of aligned reads used
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59 Number of aligned reads with deletions used to calculate the deletion
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60 profile. default=1000000
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62 Minimum mapping quality
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63 Minimum mapping quality for an alignment to be considered as "uniquely
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64 mapped". default=30
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66 Sample Output
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67 ++++++++++++++
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69 .. image:: $PATH_TO_IMAGES/mismatch_profile.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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78 </help>
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79 <expand macro="citations"/>
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80 </tool>