Mercurial > repos > iuc > vsnp_statistics
annotate vsnp_statistics.xml @ 2:b960f47c57a1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
author | iuc |
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date | Tue, 16 Nov 2021 20:12:13 +0000 |
parents | 50f539302bf4 |
children | a2f69b1598e0 |
rev | line source |
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2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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1 <tool id="vsnp_statistics" name="vSNP: statistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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2 <description></description> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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3 <macros> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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4 <import>macros.xml</import> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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5 </macros> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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6 <requirements> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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7 <expand macro="biopython_requirement"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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8 <expand macro="numpy_requirement"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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9 <expand macro="openpyxl_requirement"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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10 <expand macro="pandas_requirement"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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11 <expand macro="xlrd_requirement"/> |
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50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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12 </requirements> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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13 <command detect_errors="exit_code"><![CDATA[ |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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14 #import re |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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15 |
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b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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16 #if $input_type_cond.input_type in ["single", "pair"]: |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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17 #set read1 = $input_type_cond.read1 |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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18 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier)) |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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19 ln -s '${read1}' '${read1_identifier}' && |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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20 #if $input_type_cond.input_type == "pair": |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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21 #set read2 = $input_type_cond.read2 |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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22 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier)) |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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23 ln -s '${read2}' '${read2_identifier}' && |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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24 #end if |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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25 #else: |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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26 #set identifier = re.sub('[^\s\w\-]', '_', str($input_type_cond.reads_collection.element_identifier)) |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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27 #set read1 = $input_type_cond.reads_collection.forward |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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28 #set read1_identifier = $identifier + '_R1' |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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29 ln -s '${read1}' '${read1_identifier}' && |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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30 #set read2 = $input_type_cond.reads_collection.reverse |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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31 #set read2_identifier = $identifier + '_R2' |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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32 ln -s '${read2}' '${read2_identifier}' && |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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33 #end if |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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34 |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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35 python '$__tool_directory__/vsnp_statistics.py' |
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b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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36 --read1 '${read1_identifier}' |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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37 #if $input_type_cond.input_type in ["pair", "paired"]: |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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38 --read2 '${read2_identifier}' |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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39 #end if |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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40 #if $read1.is_of_type('fastqsanger.gz'): |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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41 --gzipped |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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42 #end if |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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43 --dbkey '$samtools_idxstats.metadata.dbkey' |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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44 --samtools_idxstats '$samtools_idxstats' |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
parents:
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45 --vsnp_azc_metrics '$vsnp_azc_metrics' |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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46 --output '$output' |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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47 ]]></command> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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48 <inputs> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
parents:
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49 <conditional name="input_type_cond"> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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50 <param name="input_type" type="select" label="Choose the category of the files to be analyzed"> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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51 <option value="single" selected="true">Single files</option> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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52 <option value="paired">Paired reads</option> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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53 <option value="pair">Paired reads in separate data sets</option> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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54 </param> |
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b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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55 <when value="single"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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56 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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57 </when> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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58 <when value="paired"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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59 <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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60 </when> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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61 <when value="pair"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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62 <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Read1 fastq file"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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63 <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Read2 fastq file"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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64 </when> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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65 </conditional> |
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b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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66 <param name="samtools_idxstats" type="data" format="tabular" label="Samtools idxstats file"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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67 <param name="vsnp_azc_metrics" type="data" format="tabular" label="vSNP: add zero coverage metrics file"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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68 </inputs> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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69 <outputs> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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70 <data name="output" format="tabular"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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71 </outputs> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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72 <tests> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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73 <!-- A single fastq file --> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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74 <test expect_num_outputs="1"> |
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b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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75 <param name="input_type" value="single"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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76 <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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77 <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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78 <param name="vsnp_azc_metrics" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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79 <output name="output" ftype="tabular"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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80 <assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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81 <has_size value="332"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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82 </assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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83 </output> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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84 </test> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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85 <!-- A set of paired fastq files --> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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86 <test expect_num_outputs="1"> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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87 <param name="input_type" value="pair"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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88 <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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89 <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
iuc
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90 <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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91 <param name="vsnp_azc_metrics" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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92 <output name="output" ftype="tabular"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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93 <assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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94 <has_size value="500"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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95 </assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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96 </output> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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97 </test> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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98 <!-- A collection of paired fastq files --> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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99 <test expect_num_outputs="1"> |
2
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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100 <param name="input_type" value="paired"/> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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101 <param name="reads_collection"> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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102 <collection type="paired"> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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103 <element name="forward" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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104 <element name="reverse" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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105 </collection> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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106 </param> |
2
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
iuc
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107 <param name="samtools_idxstats" value="samtools_idxstats5.tabular" ftype="tabular" dbkey="89"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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108 <param name="vsnp_azc_metrics" value="add_zc_metrics5.tabular" ftype="tabular" dbkey="89"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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109 <output name="output" ftype="tabular"> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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110 <assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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111 <has_size value="466"/> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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112 </assert_contents> |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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113 </output> |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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114 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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115 </tests> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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116 <help> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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117 **What it does** |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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118 |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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119 Accepts associated fastq files, SAMtools idxstats files and **vSNP: add zero coverage** metrics files and extracts information from them |
2
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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120 to produce a tabular file containing statistics for each sample. The samples can be a single read, a single set of paired reads in |
b960f47c57a1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 2a94c64d6c7236550bf483d2ffc4e86248c63aab"
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121 separate datasets or a collection of paired reads. The output statistics include reference, file size, mean read length, mean read quality, |
0
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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122 reads passing Q30, total reads, all mapped reads, unmapped reads, unmapped reads percentage of total, reference with coverage, average depth |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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123 of coverage and good SNP count. |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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124 </help> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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125 <expand macro="citations"/> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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126 </tool> |
50f539302bf4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 92f46d4bb55b582f05ac3c4b094307f114cbf98f"
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127 |