Mercurial > repos > iuc > sinto_barcode
annotate sinto_barcode.xml @ 0:3780db0073f0 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 11:03:48 +0000 |
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children | d1b34ac42b8f |
rev | line source |
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0
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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1 <tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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2 <description>add cell barcodes to FASTQ read names</description> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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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> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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5 </macros> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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6 <requirements> |
3780db0073f0
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> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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8 </requirements> |
3780db0073f0
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 '$barcode_fastq' barcodes.fastq.gz && |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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12 ln -s '${fastq_input.read1_fastq}' read1.fastq.gz && |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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13 #if str( $fastq_input.fastq_input_selector ) == "paired": |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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14 ln -s '${fastq_input.read2_fastq}' read2.fastq.gz && |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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15 #end if |
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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 sinto barcode |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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17 --barcode_fastq barcodes.fastq.gz |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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18 --read1 read1.fastq.gz |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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19 #if str( $fastq_input.fastq_input_selector ) == "paired": |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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20 --read2 read2.fastq.gz |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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21 #end if |
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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 --bases $bases |
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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 ]]> </command> |
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24 <inputs> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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25 <param type="data" name="barcode_fastq" format="fastqsanger.gz" label="FASTQ file containing cell barcode sequences" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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26 <conditional name="fastq_input"> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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27 <param name="fastq_input_selector" type="select" label="Single or Paired-end data"> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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28 <option value="paired">Paired</option> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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29 <option value="single">Single</option> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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30 </param> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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31 <when value="paired"> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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32 <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Forward reads FASTQ file" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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33 <param name="read2_fastq" type="data" format="fastqsanger.gz" label="Reverse reads FASTQ file" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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34 </when> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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35 <when value="single"> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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36 <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Select FASTQ file" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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37 </when> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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38 </conditional> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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39 <param type="integer" name="bases" value="16" min="0" label="Number of bases to extract from barcode-containing FASTQ" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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40 </inputs> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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41 <outputs> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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42 <data name='read1_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 1" from_work_dir="read1.barcoded.fastq" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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43 <data name='read2_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 2" from_work_dir="read2.barcoded.fastq" > |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
iuc
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44 <filter>fastq_input['fastq_input_selector'] == 'paired'</filter> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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45 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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46 </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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47 <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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48 <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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49 <param name="barcode_fastq" value="barcodes.fastq.gz" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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50 <param name="fastq_input_selector" value="single"/> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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51 <param name="read1_fastq" value="read1.fastq.gz" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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52 <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> |
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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 </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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54 <test expect_num_outputs="2"> |
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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 <param name="barcode_fastq" value="barcodes.fastq.gz" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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56 <param name="fastq_input_selector" value="paired"/> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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57 <param name="read1_fastq" value="read1.fastq.gz" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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58 <param name="read2_fastq" value="read2.fastq.gz" /> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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59 <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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60 <output name="read2_out" file="read2.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/> |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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61 </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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62 </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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63 <help><![CDATA[ |
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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 |
3780db0073f0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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65 Sinto is a toolkit for processing aligned single-cell data. |
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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 -------------------------------------------------------------------------------------------------------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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67 Cell barcodes from one FASTQ file added to the read names of another, or the same, FASTQ file. This is useful when processing raw single-cell sequencing data, as the cell barcode information can easily be propagated to the aligned BAM file by encoding the cell barcode in the read name. |
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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 |
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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 **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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70 FASTQ files containing barcodes and forward reads. An optional reverse reads FASTQ file can be provided for paired-end experiments. Note that all the FASTQs must contain the same number of reads and the reads must appear in the same order. |
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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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71 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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72 **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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73 FASTQ files with the read names modified to contain the cell barcode sequence at the beginning of the read name, separated from the original read name by a : character. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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74 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
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75 ]]> </help> |
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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 <expand macro="citations" /> |
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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 </tool> |