Mercurial > repos > iuc > sinto_fragments
annotate sinto_fragments.xml @ 0:b6009d0098d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
author | iuc |
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date | Thu, 13 Apr 2023 11:03:34 +0000 |
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children | 02f96be6c3c9 |
rev | line source |
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0
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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1 <tool id="sinto_fragments" name="Sinto fragments" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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2 <description>Create an ATAC-seq fragment file from a BAM file</description> |
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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4 <import>macros.xml</import> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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5 </macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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6 <requirements> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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7 <requirement type="package" version="@TOOL_VERSION@">sinto</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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8 </requirements> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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9 <version_command>sinto --version</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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10 <command><![CDATA[ |
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11 ln -s '$bam' 'input.bam' && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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12 ln -s '$bam.metadata.bam_index' 'input.bam.bai' && |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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13 sinto fragments |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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14 --bam 'input.bam' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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15 --min_mapq $min_mapq |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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16 --barcodetag '$barcodetag' |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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17 --barcode_regex '${ str( $barcode_regex ) }' |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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18 --max_distance $max_distance |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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19 --min_distance $min_distance |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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20 --shift_plus $shift_plus |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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21 --shift_minus $shift_minus |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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22 $collapse_within |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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23 --fragments $fragments |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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24 --nproc "\${GALAXY_SLOTS:-1}" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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25 ]]> </command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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26 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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27 <param argument="--bam" type="data" format="bam" label="Input BAM file" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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28 <param argument="--min_mapq" type="integer" value="30" min="0" label="Minimum MAPQ required to retain fragment" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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29 <param argument="--barcodetag" type="text" value="CB" label="Read tag storing cell barcode information" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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30 <param argument="--barcode_regex" type="text" value="[^:]*" label="Read tag storing cell barcode information" |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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31 help="[^:]* matches all characters up to the first colon" > |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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32 <sanitizer> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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33 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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34 <remove value="'" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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35 </valid> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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36 </sanitizer> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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37 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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38 <param argument="--max_distance" type="integer" value="5000" min="0" label="Maximum distance between integration sites for the fragment to be retained" |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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39 help="Allows filtering of implausible fragments that likely result from incorrect mapping positions. Default is 5000 bp."/> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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40 <param argument="--min_distance" type="integer" value="10" min="0" label="Minimum distance between integration sites for the fragment to be retained" |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
parents:
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41 help="Allows filtering of implausible fragments that likely result from incorrect mapping positions. Default is 5000 bp."/> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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42 <param argument="--shift_plus" type="integer" value="4" label="Minimum MAPQ required to retain fragment" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
parents:
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43 <param argument="--shift_minus" type="integer" value="-5" label="Minimum MAPQ required to retain fragment" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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44 <param argument="--collapse_within" type="boolean" truevalue="--collapse_within" falsevalue="" label="Take cell barcode into account |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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45 when collapsing duplicate fragments" help="Setting this flag means that fragments with the same coordinates can be identified |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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46 provided they originate from a different cell barcode." /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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47 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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48 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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49 <data name='fragments' format='bed' label="${tool.name} on ${on_string}: fragments" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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50 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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51 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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52 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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53 <param name="bam" ftype="bam" value="aligned.bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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54 <output name="fragments"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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55 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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56 <has_text_matching expression="chrY\t2790323\t2790683\tAACTGGTAGCTCCGGT\t2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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57 <has_text_matching expression="chrY\t3680091\t3680228\tGACCGACGTACGGTTT\t2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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58 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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59 </output> |
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60 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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61 <test expect_num_outputs="1"> |
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62 <param name="bam" ftype="bam" value="aligned.bam" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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63 <param name="shift_plus" value="4" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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64 <param name="shift_minus" value="5" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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65 <output name="fragments"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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66 <assert_contents> |
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67 <has_text_matching expression="chrY\t2790323\t2790693\tAACTGGTAGCTCCGGT\t2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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68 <has_text_matching expression="chrY\t3680091\t3680238\tGACCGACGTACGGTTT\t2" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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69 </assert_contents> |
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70 </output> |
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71 </test> |
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72 </tests> |
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73 <help><![CDATA[ |
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74 |
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75 Sinto: single-cell analysis tools |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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76 -------------------------------------------------------------------------------------------------------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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77 An ATAC-seq fragment file can be created from a BAM file using the fragments command. The fragment file contains the position of each |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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78 Tn5 integration site, the cell barcode associated with the fragment, and the number of times the fragment was sequenced. PCR duplicates are collapsed. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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79 |
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80 **Input** |
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81 A BAM file. Alignments in the input BAM file must contain cell barcodes either as a part of read names or in a tag (typically, in CB tag). |
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82 |
b6009d0098d7
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83 **Output** |
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84 The fragment file. It contains the positions of Tn5 integration sites, the cell barcode that the DNA fragment originated from, and the number of times |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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85 the fragment was sequenced. |
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86 |
b6009d0098d7
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87 ]]> </help> |
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88 <expand macro="citations" /> |
b6009d0098d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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89 </tool> |