Mercurial > repos > iuc > cite_seq_count
annotate cite_seq_count.xml @ 0:3df3d1b51110 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
author | iuc |
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date | Wed, 18 Jan 2023 16:04:20 +0000 |
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3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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1 <tool name="CITE-seq-Count" id="cite_seq_count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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2 <description>Count CMO/HTO</description> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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3 <macros> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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4 <token name="@TOOL_VERSION@">1.4.4</token> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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5 <token name="@VERSION_SUFFIX@">0</token> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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6 </macros> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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7 <edam_topics> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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8 <edam_topic>topic_3170</edam_topic> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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9 <edam_topic>topic_4028</edam_topic> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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10 <edam_topic>topic_3308</edam_topic> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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11 </edam_topics> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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12 <xrefs> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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13 <xref type="bio.tools">CITE-seq-Count</xref> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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14 </xrefs> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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15 <requirements> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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16 <requirement type="package" version="@TOOL_VERSION@">cite-seq-count</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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17 <requirement type="package" version="3.7.12">python</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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18 <requirement type="package" version="1.0.0">umi_tools</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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19 <requirement type="package" version="0.20.7">python-levenshtein</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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20 <requirement type="package" version="0.20.7">levenshtein</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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21 <requirement type="package" version="0.25.3">pandas</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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22 <requirement type="package" version="1.0.0">umi_tools</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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23 <!-- The next dependencies are here to help conda to solve the environment --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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24 <requirement type="package" version="1.0.8">bzip2</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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25 <requirement type="package" version="2.5.0">expat</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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26 <requirement type="package" version="0.70.14">multiprocess</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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27 <requirement type="package" version="1.21.6">numpy</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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28 <requirement type="package" version="0.16">pysam</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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29 <requirement type="package" version="1.7.3">scipy</requirement> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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30 </requirements> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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31 <stdio> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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32 <exit_code range="1:" level="fatal"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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33 </stdio> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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34 <version_command>CITE-seq-Count --version</version_command> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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35 <command><![CDATA[ |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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36 ## This is taken from the star solo wrapper: |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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37 ## Check that the input pairs are of the same type. |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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38 ## We consume either repeats of two inputs R1 + R2 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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39 ## or a collection of paired reads. |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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40 #if str($input_types.use) == "repeat": |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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41 #assert len(str($input_types.input1).split(",")) == len(str($input_types.input2).split(",")) |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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42 #set $reads1 = $input_types.input1 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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43 #set $reads2 = $input_types.input2 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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44 #elif str($input_types.use) == "list_paired": |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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45 #set $reads1 = $input_types.input_collection.forward |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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46 #set $reads2 = $input_types.input_collection.reverse |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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47 #end if |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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48 CITE-seq-Count |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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49 --threads \${GALAXY_SLOTS:-4} |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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50 --read1 '$reads1' |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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51 --read2 '$reads2' |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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52 --tags '$tags' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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53 ## Chemistry: |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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54 #if str($params.chemistry) == "v2": |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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55 --cell_barcode_first_base 1 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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56 --cell_barcode_last_base 16 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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57 --umi_first_base 17 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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58 --umi_last_base 26 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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59 #else if str($params.chemistry) == "v3": |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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60 --cell_barcode_first_base 1 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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61 --cell_barcode_last_base 16 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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62 --umi_first_base 17 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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63 --umi_last_base 28 |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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64 #else if str($params.chemistry) == "custom": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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65 --cell_barcode_first_base $params.cell_barcode_first_base |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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66 --cell_barcode_last_base $params.cell_barcode_last_base |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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67 --umi_first_base $params.umi_first_base |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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68 --umi_last_base $params.umi_last_base |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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69 #end if |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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70 --bc_collapsing_dist $bc_collapsing_dist |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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71 --umi_collapsing_dist $umi_collapsing_dist |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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72 $no_umi_correction |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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73 --expected_cells $expected_cells |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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74 #if $whitelist: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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75 --whitelist '$whitelist' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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76 #end if |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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77 --max-error $max_error |
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78 #if str($start_trim) != "0": |
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79 --start-trim $start_trim |
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80 #end if |
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81 $sliding_window |
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82 $dense |
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83 #if str($first_n) != "0": |
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84 --first_n $first_n |
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85 #end if |
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86 #if str($unmapped.output) == "true": |
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87 --unknown-top-tags $unknown_top_tags |
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88 #end if |
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89 |
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90 ## Outputs are gzip |
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91 && gunzip Results/read_count/barcodes.tsv.gz |
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92 && gunzip Results/read_count/features.tsv.gz |
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93 && gunzip Results/read_count/matrix.mtx.gz |
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94 && gunzip Results/umi_count/barcodes.tsv.gz |
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95 && gunzip Results/umi_count/features.tsv.gz |
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96 && gunzip Results/umi_count/matrix.mtx.gz |
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97 ]]> |
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98 </command> |
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99 <inputs> |
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100 <conditional name="input_types" > |
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101 <param name="use" type="select" label="Input Type" > |
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102 <option value="repeat" >Separate barcode and CMO/HTO reads</option> |
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103 <option value="list_paired" >Paired collection of barcode and CMO/HTO reads</option> |
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104 </param> |
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105 <when value="repeat"> |
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106 <param format="fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true" |
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107 label="RNA-Seq FASTQ file, Barcode reads" /> |
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108 <param format="fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true" |
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109 label="RNA-Seq FASTQ file, HTO/CMO reads"/> |
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110 </when> |
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111 <when value="list_paired"> |
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112 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq.gz,fastqsanger.gz" label="Collection of Pairs" /> |
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113 </when> |
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114 </conditional> |
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115 <param argument="--tags" type="data" format="csv" label="the CMO/HTO barcodes as well as their respective names" help="first column is the sequence and second column is the name" /> |
3df3d1b51110
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116 <conditional name="params" > |
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117 <param name="chemistry" type="select" label="Configure Chemistry Options"> |
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118 <option value="v2" selected="true">Chromium Chemistry v2</option> |
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119 <option value="v3">Chromium Chemistry v3</option> |
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120 <option value="custom">Custom</option> |
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121 </param> |
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122 <when value="v2" /> |
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123 <when value="v3" /> |
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124 <when value="custom" > |
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125 <param argument="--cell_barcode_first_base" type="integer" min="1" value="1" label="Cell Barcode First Base" /> |
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126 <param argument="--cell_barcode_last_base" type="integer" min="1" value="16" label="Cell Barcode Last Base" /> |
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127 <param argument="--umi_first_base" type="integer" min="1" value="17" label="UMI First Base" /> |
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128 <param argument="--umi_last_base" type="integer" min="1" value="26" label="UMI Last Base" /> |
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129 </when> |
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130 </conditional> |
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131 <param argument="--bc_collapsing_dist" type="integer" min="0" value="1" label="How many errors are allowed between two cell barcodes to collapse them onto one cell." /> |
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132 <param argument="--umi_collapsing_dist" type="integer" min="0" value="2" label="How many errors are allowed between two umi within the same cell and TAG to collapse." /> |
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133 <param argument="--no_umi_correction" type="boolean" truevalue="--no_umi_correction" falsevalue="" checked="false" label="Deactivate UMI correction" /> |
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134 <param argument="--expected_cells" type="integer" min="1" value="3000" label="How many cells you expect in your run" /> |
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135 <param argument="--whitelist" type="data" format="txt,csv,tsv" label="Whitelist of cell barcodes" optional="true"/> |
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136 <param name="max_error" type="integer" min="0" value="2" label="Maximum Levenshtein distance allowed for CMO/HTO."/> |
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137 <param name="start_trim" type="integer" min="0" value="0" label="How many bases should be trimmed on CMO/HTO read before starting to map"/> |
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138 <param name="sliding_window" type="boolean" truevalue="--sliding-window" falsevalue="" checked="false" label="Activate sliding window alignement."/> |
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139 <param argument="--dense" type="boolean" truevalue="--dense" falsevalue="" checked="false" label="Output in tsv format (in addition to the dense format)"/> |
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140 <param argument="--first_n" type="integer" value="0" label="Select N reads to run on instead of all." /> |
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141 <conditional name="unmapped"> |
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142 <param name="output" type="select" label="Write table of unknown TAGs to file."> |
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143 <option value="false">No</option> |
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144 <option value="true">Yes</option> |
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145 </param> |
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146 <when value="false"/> |
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147 <when value="true"> |
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148 <param name="unknown_top_tags" type="integer" min="1" value="100" label="Top n unmapped TAGs to output."/> |
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149 </when> |
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150 </conditional> |
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151 </inputs> |
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152 <outputs> |
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153 <data name="report" format="yaml" label="${tool.name} on ${on_string}: report" from_work_dir="Results/run_report.yaml" /> |
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154 <data format="tsv" name="output_features" label="${tool.name} on ${on_string}: Features raw" |
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155 from_work_dir="Results/read_count/features.tsv" /> |
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156 <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes raw" |
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157 from_work_dir="Results/read_count/barcodes.tsv" /> |
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158 <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Features Counts raw" |
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159 from_work_dir="Results/read_count/matrix.mtx" /> |
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160 <data format="tsv" name="output_features_filtered" label="${tool.name} on ${on_string}: Features filtered" |
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161 from_work_dir="Results/umi_count/features.tsv" /> |
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162 <data format="tsv" name="output_barcodes_filtered" label="${tool.name} on ${on_string}: Barcodes filtered" |
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163 from_work_dir="Results/umi_count/barcodes.tsv" /> |
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164 <data format="mtx" name="output_matrix_filtered" label="${tool.name} on ${on_string}: Matrix Features Counts filtered (UMI)" |
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165 from_work_dir="Results/umi_count/matrix.mtx" /> |
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166 <data format="tsv" name="dense_output_matrix" label="${tool.name} on ${on_string}: Dense Matrix With UMI" |
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167 from_work_dir="Results/dense_umis.tsv" > |
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168 <filter>dense</filter> |
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169 </data> |
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170 </outputs> |
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171 <tests> |
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172 <test expect_num_outputs="7"> |
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173 <!-- test 1 --> |
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174 <param name="tags" value="tags.csv"/> |
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175 <param name="expected_cells" value="2"/> |
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176 <param name="whitelist" value="whitelist.txt"/> |
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177 <conditional name="input_types"> |
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178 <param name="use" value="repeat"/> |
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179 <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/> |
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180 <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/> |
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181 </conditional> |
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182 <conditional name="params" > |
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183 <param name="chemistry" value="v2"/> |
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184 </conditional> |
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185 <output name="report"> |
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186 <assert_contents> |
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187 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
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188 <has_line line="Reads processed: 200"/> |
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189 <has_line line="Uncorrected cells: 0"/> |
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190 </assert_contents> |
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191 </output> |
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192 <output name="output_barcodes"> |
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193 <assert_contents> |
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194 <has_line line="TAGAGGGAAGTCAAGC"/> |
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195 <has_line line="TACATATTCTTTACTG"/> |
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196 <has_n_lines n="4"/> |
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197 </assert_contents> |
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198 </output> |
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199 <output name="output_features"> |
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200 <assert_contents> |
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201 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
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202 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
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203 <has_line line="unmapped"/> |
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204 <has_n_lines n="3"/> |
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205 </assert_contents> |
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206 </output> |
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207 <output name="output_matrix"> |
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208 <assert_contents> |
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209 <has_line_matching expression="[1-2]\s+[1-4]\s+43"/> |
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210 <has_n_lines n="9"/> |
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211 </assert_contents> |
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212 </output> |
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213 <output name="output_barcodes_filtered"> |
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214 <assert_contents> |
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215 <has_line line="TAGAGGGAAGTCAAGC"/> |
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216 <has_line line="TACATATTCTTTACTG"/> |
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217 <has_n_lines n="4"/> |
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218 </assert_contents> |
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219 </output> |
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220 <output name="output_features_filtered"> |
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221 <assert_contents> |
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222 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
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223 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
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224 <has_line line="unmapped"/> |
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225 <has_n_lines n="3"/> |
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226 </assert_contents> |
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227 </output> |
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228 <output name="output_matrix_filtered"> |
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229 <assert_contents> |
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230 <has_line_matching expression="[1-2]\s+[1-4]\s+36"/> |
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231 <has_n_lines n="9"/> |
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232 </assert_contents> |
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233 </output> |
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234 </test> |
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235 <test expect_num_outputs="8"> |
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236 <!-- test 2 --> |
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237 <!-- change input style use dense no whitelist--> |
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238 <param name="tags" value="tags.csv"/> |
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239 <param name="expected_cells" value="2"/> |
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240 <conditional name="input_types"> |
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241 <param name="use" value="list_paired" /> |
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242 <param name="input_collection" > |
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243 <collection type="paired"> |
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244 <element name="forward" value="correct_R1.fastq.gz" ftype="fastqsanger.gz" /> |
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245 <element name="reverse" value="correct_R2.fastq.gz" ftype="fastqsanger.gz" /> |
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246 </collection> |
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247 </param> |
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248 </conditional> |
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249 <conditional name="params" > |
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250 <param name="chemistry" value="v2"/> |
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251 </conditional> |
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252 <param name="dense" value="true"/> |
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253 <output name="report"> |
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254 <assert_contents> |
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255 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
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256 <has_line line="Reads processed: 200"/> |
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257 <has_line line="Uncorrected cells: 0"/> |
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258 </assert_contents> |
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259 </output> |
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260 <output name="output_barcodes"> |
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261 <assert_contents> |
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262 <has_line line="TAGAGGGAAGTCAAGC"/> |
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263 <has_line line="TACATATTCTTTACTG"/> |
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264 <has_n_lines n="2"/> |
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265 </assert_contents> |
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266 </output> |
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267 <output name="output_features"> |
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268 <assert_contents> |
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269 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
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270 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
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271 <has_line line="unmapped"/> |
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272 <has_n_lines n="3"/> |
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273 </assert_contents> |
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274 </output> |
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275 <output name="output_matrix"> |
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276 <assert_contents> |
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277 <has_line_matching expression="[1-2]\s+[1-2]\s+43"/> |
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278 <has_n_lines n="9"/> |
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279 </assert_contents> |
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280 </output> |
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281 <output name="output_barcodes_filtered"> |
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282 <assert_contents> |
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283 <has_line line="TAGAGGGAAGTCAAGC"/> |
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284 <has_line line="TACATATTCTTTACTG"/> |
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285 <has_n_lines n="2"/> |
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286 </assert_contents> |
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287 </output> |
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288 <output name="output_features_filtered"> |
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289 <assert_contents> |
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290 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
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291 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
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292 <has_line line="unmapped"/> |
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293 <has_n_lines n="3"/> |
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294 </assert_contents> |
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295 </output> |
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296 <output name="output_matrix_filtered"> |
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297 <assert_contents> |
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298 <has_line_matching expression="[1-2]\s+[1-2]\s+36"/> |
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299 <has_n_lines n="9"/> |
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300 </assert_contents> |
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301 </output> |
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302 <output name="dense_output_matrix"> |
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303 <assert_contents> |
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304 <has_line_matching expression="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC\s+2[79]\s+2[79]"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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305 <has_line_matching expression="test1-CGTAGCTCG-CGTAGCTCG\s+[23][56]\s+[23][56]"/> |
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306 <has_line_matching expression="unmapped\s+2[17]\s+2[17]"/> |
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307 <has_n_lines n="4"/> |
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308 </assert_contents> |
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309 </output> |
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310 </test> |
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311 <test expect_num_outputs="7"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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312 <!-- test 3 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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diff
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313 <!-- custom chemistry max_error 5 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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314 <param name="tags" value="tags.csv"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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315 <param name="expected_cells" value="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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316 <param name="whitelist" value="whitelist.txt"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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317 <conditional name="input_types"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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318 <param name="use" value="repeat"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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319 <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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diff
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320 <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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321 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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diff
changeset
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322 <conditional name="params" > |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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323 <param name="chemistry" value="custom"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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324 <param name="cell_barcode_first_base" value="1"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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325 <param name="cell_barcode_last_base" value="16"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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326 <param name="umi_first_base" value="17"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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327 <param name="umi_last_base" value="26"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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328 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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329 <param name="max_error" value="5"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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330 <output name="report"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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331 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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332 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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333 <has_line line="Reads processed: 200"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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334 <has_line line="Uncorrected cells: 0"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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335 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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336 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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337 <output name="output_barcodes"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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338 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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339 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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340 <has_line line="TACATATTCTTTACTG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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341 <has_n_lines n="4"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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342 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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343 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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344 <output name="output_features"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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345 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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346 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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347 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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348 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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349 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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350 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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351 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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352 <output name="output_matrix"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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353 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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354 <has_line_matching expression="[1-2]\s+[1-4]\s+68"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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355 <has_n_lines n="7"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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356 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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357 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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358 <output name="output_barcodes_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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diff
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359 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
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360 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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361 <has_line line="TACATATTCTTTACTG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
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362 <has_n_lines n="4"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
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363 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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364 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
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365 <output name="output_features_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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366 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
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367 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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368 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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369 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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370 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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371 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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372 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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373 <output name="output_matrix_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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374 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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375 <has_line_matching expression="[1-2]\s+[1-4]\s+52"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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376 <has_n_lines n="7"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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377 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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378 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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379 </test> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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380 <test expect_num_outputs="7"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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381 <!-- test 4 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
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parents:
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382 <!-- incompatible whitelist --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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383 <param name="tags" value="tags.csv"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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384 <param name="expected_cells" value="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
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385 <param name="whitelist" value="incompatible_whitelist.txt"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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386 <conditional name="input_types"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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387 <param name="use" value="repeat"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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388 <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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389 <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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390 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
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391 <conditional name="params" > |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
392 <param name="chemistry" value="v2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
393 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
394 <output name="report"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
395 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
396 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
397 <has_line line="Reads processed: 200"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
398 <has_line line="Uncorrected cells: 0"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
399 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
400 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
401 <output name="output_barcodes"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
402 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
403 <has_line line="AAAAAAAAAAAAAAAA"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
404 <has_line line="TTTTTTTTTTTTTTTT"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
405 <has_n_lines n="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
406 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
407 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
408 <output name="output_features"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
409 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
410 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
411 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
412 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
413 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
414 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
415 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
416 <output name="output_matrix"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
417 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
418 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
419 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
420 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
421 <output name="output_barcodes_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
422 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
423 <has_line line="AAAAAAAAAAAAAAAA"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
424 <has_line line="TTTTTTTTTTTTTTTT"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
425 <has_n_lines n="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
426 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
427 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
428 <output name="output_features_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
429 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
430 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
431 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
432 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
433 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
434 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
435 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
436 <output name="output_matrix_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
437 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
438 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
439 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
440 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
441 </test> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
442 <test expect_num_outputs="7"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
443 <!-- test 5 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
444 <!-- umi_collapsing_dist 5 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
445 <param name="tags" value="tags.csv"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
446 <param name="expected_cells" value="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
447 <param name="whitelist" value="whitelist.txt"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
448 <conditional name="input_types"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
449 <param name="use" value="repeat"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
450 <param name="input1" value="correct_R1.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
451 <param name="input2" value="correct_R2.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
452 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
453 <conditional name="params" > |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
454 <param name="chemistry" value="v2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
455 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
456 <param name="umi_collapsing_dist" value="5"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
457 <output name="report"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
458 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
459 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
460 <has_line line="Reads processed: 200"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
461 <has_line line="Uncorrected cells: 0"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
462 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
463 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
464 <output name="output_barcodes"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
465 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
466 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
467 <has_line line="TACATATTCTTTACTG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
468 <has_n_lines n="4"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
469 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
470 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
471 <output name="output_features"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
472 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
473 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
474 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
475 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
476 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
477 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
478 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
479 <output name="output_matrix"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
480 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
481 <has_line_matching expression="[1-2]\s+[1-4]\s+43"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
482 <has_n_lines n="9"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
483 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
484 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
485 <output name="output_barcodes_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
486 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
487 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
488 <has_line line="TACATATTCTTTACTG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
489 <has_n_lines n="4"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
490 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
491 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
492 <output name="output_features_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
493 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
494 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
495 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
496 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
497 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
498 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
499 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
500 <output name="output_matrix_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
501 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
502 <has_line_matching expression="[1-2]\s+[1-4]\s+10"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
503 <has_n_lines n="9"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
504 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
505 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
506 </test> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
507 <test expect_num_outputs="7"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
508 <!-- test 6 --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
509 <!-- multiple fastqs --> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
510 <param name="tags" value="tags.csv"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
511 <param name="expected_cells" value="2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
512 <param name="whitelist" value="whitelist.txt"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
513 <conditional name="input_types"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
514 <param name="use" value="repeat"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
515 <param name="input1" value="correct_R1.fastq.gz,correct_R1.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
516 <param name="input2" value="correct_R2.fastq.gz,correct_R2.fastq.gz" ftype="fastqsanger.gz"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
517 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
518 <conditional name="params" > |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
519 <param name="chemistry" value="v2"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
520 </conditional> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
521 <output name="report"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
522 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
523 <has_line line="CITE-seq-Count Version: @TOOL_VERSION@"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
524 <has_line line="Reads processed: 400"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
525 <has_line line="Uncorrected cells: 0"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
526 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
527 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
528 <output name="output_barcodes"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
529 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
530 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
531 <has_line line="TACATATTCTTTACTG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
532 <has_n_lines n="4"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
533 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
534 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
535 <output name="output_features"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
536 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
537 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
538 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
539 <has_line line="unmapped"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
540 <has_n_lines n="3"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
541 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
542 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
543 <output name="output_matrix"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
544 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
545 <has_line_matching expression="[1-2]\s+[1-4]\s+86"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
546 <has_n_lines n="9"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
547 </assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
548 </output> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
549 <output name="output_barcodes_filtered"> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
550 <assert_contents> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
551 <has_line line="TAGAGGGAAGTCAAGC"/> |
3df3d1b51110
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count commit 70fe293f480c4d0e9f14d4373ecac4cbcf4fe17f
iuc
parents:
diff
changeset
|
552 <has_line line="TACATATTCTTTACTG"/> |
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553 <has_n_lines n="4"/> |
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554 </assert_contents> |
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555 </output> |
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556 <output name="output_features_filtered"> |
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557 <assert_contents> |
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558 <has_line line="test2-CGTACGTAGCCTAGC-CGTACGTAGCCTAGC"/> |
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559 <has_line line="test1-CGTAGCTCG-CGTAGCTCG"/> |
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560 <has_line line="unmapped"/> |
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561 <has_n_lines n="3"/> |
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562 </assert_contents> |
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563 </output> |
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564 <output name="output_matrix_filtered"> |
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565 <assert_contents> |
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566 <has_line_matching expression="[1-2]\s+[1-4]\s+36"/> |
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567 <has_n_lines n="9"/> |
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568 </assert_contents> |
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569 </output> |
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570 </test> |
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571 </tests> |
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572 <help><![CDATA[ |
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573 CITE-seq-Count is a program that outputs UMI and read counts from raw fastq CITE-seq or hashing data. |
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574 |
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575 Here is an image explaining the expected structure of read1 and read2 from the sequencer: |
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576 |
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577 .. image:: read_structure.png |
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578 :alt: Read1: --barcode--|--umi--|TTTT and Read2: --CMO/HTO--|AAA |
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579 |
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580 ]]></help> |
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581 <citations> |
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582 <citation type="doi">10.5281/zenodo.2585469</citation> |
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583 </citations> |
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584 </tool> |