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annotate bamparse.xml @ 4:1997af8f4648 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
author artbio
date Thu, 20 Jul 2023 00:32:36 +0000
parents 120eb76aa500
children 320f7746b9f5
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4
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
artbio
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1 <tool id="bamparse" name="Count alignments" version="4.1.0">
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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2 <description>in a BAM file</description>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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3 <requirements>
3
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
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4 <requirement type="package" version="0.21.0=py310h41dec4a_1">pysam</requirement>
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
artbio
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5 <requirement type="package" version="1.0=h98b6b92_0">sambamba</requirement>
120eb76aa500 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e8a19ac6ada887e6daa0a2e2abc9ba69392cdb8a
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6 <requirement type="package" version="1.17=hd87286a_1">samtools</requirement>
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2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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7 </requirements>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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8 <stdio>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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9 <exit_code range="1:" level="fatal" description="Tool exception" />
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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10 </stdio>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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11 <command detect_errors="exit_code"><![CDATA[
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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12 mkdir outputdir &&
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8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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13 #if $polarity == 'sense':
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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14 #set pol=' and not reverse_strand'
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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15 #else if $polarity == 'antisense':
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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16 #set pol=' and reverse_strand'
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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17 #else:
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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18 #set pol=''
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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19 #end if
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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20 #for $file in $input_list
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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21 sambamba view -t \$GALAXY_SLOTS -F "not unmapped$pol" -f bam '$file' -o '$file.element_identifier' &&
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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22 samtools index '$file.element_identifier' &&
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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23 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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24 python $__tool_directory__/bamparse.py
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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25 --alignments
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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26 #for $file in $input_list
2
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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27 '$file.element_identifier'
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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28 #end for
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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29 --labels
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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30 #for $file in $input_list
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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31 '$file.element_identifier'
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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32 #end for
4
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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33 --number '$output_option' &&
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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34 #if $output_option == 'unique':
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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35 cp ./outputdir/table.tabular $table
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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36 #else if $output_option == 'multiple':
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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37 cp outputdir/* ./ && ls -latr ./
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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38 #end if
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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39 ]]></command>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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40 <inputs>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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41 <param name="input_list" type="data" format="bam" label="Select multiple alignments to parse" multiple="true"/>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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42 <param name="polarity" type="select" label="how to count sense and antisense reads">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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43 <option value="both">count both sense and antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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44 <option value="sense">count only sense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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45 <option value="antisense">count only antisense reads</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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46 </param>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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47 <param name="output_option" type="select" display="radio" label="Select the number of files for results"
4
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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48 help="Results can be returned either as a single multi-column table or in a collection of separate two-column
0
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49 datasets (useful for DESeq subsequent analysis)">
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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50 <option value="unique">A multi-column table</option>
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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51 <option value="multiple">One separate two-columns dataset per input bam alignment</option>
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52 </param>
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53 </inputs>
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54 <outputs>
4
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55 <data name="table" format="tabular" label="Table of Counts">
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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56 <filter>output_option == "unique"</filter>
0
2a1a2bc6ae8b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 4e42cba873625fad03423e65dfffbf4afa91598c
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57 </data>
4
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58
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59 <collection name="split_output" type="list" label="Collection of Count Tables">
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60 <filter>output_option == "multiple"</filter>
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61 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.tabular" format="tabular" visible="false" directory="outputdir"/>
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62 </collection>
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63
0
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64 </outputs>
2
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65 <tests>
4
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66 <test expect_num_outputs="1">
2
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67 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
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68 <param name="polarity" value="both" />
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69 <param name="output_option" value="unique" />
4
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70 <output name="table" ftype="tabular" file="table.tabular" count="1"/>
2
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71 </test>
4
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72 <test expect_num_outputs="1">
2
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73 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
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74 <param name="polarity" value="both" />
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75 <param name="output_option" value="multiple" />
4
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76 <output_collection name="split_output" type="list" count="2">
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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77 <element name="table0" file="table0.tabular" ftype="tabular" compare="contains" />
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78 <element name="table1" file="table1.tabular" ftype="tabular" compare="contains" />
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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79 </output_collection>
2
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80 </test>
4
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81 <test expect_num_outputs="1">
2
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82 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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83 <param name="polarity" value="sense" />
8ea06787c08a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit 968c9ab925ed768027ff8012d0ff6410fc24f079
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84 <param name="output_option" value="unique" />
4
1997af8f4648 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/bamparse commit e1e871049975dff030bf1e6fe2df8b8fa8997141
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85 <output name="table" ftype="tabular" file="table.tabular" count="1"/>
2
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86 </test>
4
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87 <test expect_num_outputs="1">
2
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88 <param name="input_list" value="alignment1.bam,alignment2.bam" ftype="bam" />
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89 <param name="polarity" value="antisense" />
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90 <param name="output_option" value="unique" />
4
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91 <output name="table" ftype="tabular" file="table_antisense.tabular" count="1"/>
2
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92 </test>
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93
4
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94 <test expect_num_outputs="1">
2
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95 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
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96 <param name="polarity" value="both" />
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97 <param name="output_option" value="multiple" />
4
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98 <output_collection name="split_output" type="list" count="3">
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99 <element name="table0" file="more_table0.tabular" ftype="tabular" compare="contains" />
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100 <element name="table1" file="more_table1.tabular" ftype="tabular" compare="contains" />
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101 <element name="table2" file="more_table2.tabular" ftype="tabular" compare="contains" />
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102 </output_collection>
2
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103 </test>
4
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104 <test expect_num_outputs="1">
2
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105 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
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106 <param name="polarity" value="sense" />
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107 <param name="output_option" value="unique" />
4
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108 <output name="table" ftype="tabular" file="more_sense_table.tabular" count="1"/>
2
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109 </test>
4
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110 <test expect_num_outputs="1">
2
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111 <param name="input_list" value="input1.bam,input2.bam,input_new2.bam" ftype="bam" />
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112 <param name="polarity" value="antisense" />
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113 <param name="output_option" value="unique" />
4
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114 <output name="table" ftype="tabular" file="more_antisense_table.tabular" count="1"/>
2
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115 </test>
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116 </tests>
0
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117 <help>
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118
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119 **What it does**
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120
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121 Counts the number of reads aligned to each reference (@SN, reference NAME) in one or
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122 several BAM alignments.
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123
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124 Sense, antisense or both sense and antisense alignments can be counted
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125
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126 The library labels in the returned count table are taken from the input bam datasets
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127 names in the Galaxy history.
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128 </help>
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129 </tool>