Mercurial > repos > iuc > nextclade
annotate nextclade.xml @ 13:64be7ff9b97b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
author | iuc |
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date | Thu, 27 Jan 2022 14:04:45 +0000 |
parents | 56b1a13d9680 |
children | b60593baff7d |
rev | line source |
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0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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2 <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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3 <macros> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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4 <import>macros.xml</import> |
3
3b75d5285aff
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 7a13866c45dba2337fc37d66c45c77ac73915690"
iuc
parents:
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5 <token name="@VERSION_SUFFIX@">0</token> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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6 </macros> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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7 <requirements> |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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8 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement> |
6
1e0234b87809
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 475d00042b5ec4216fa1e5f52e3ec0cf25c67707"
iuc
parents:
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9 <requirement type="package" version="8.31">coreutils</requirement> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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10 </requirements> |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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11 <version_command>nextclade --version-detailed</version_command> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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12 <command detect_errors="exit_code"><![CDATA[ |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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13 nextclade dataset get -n '${organism}' -o db && |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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14 nextclade run |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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15 --input-fasta '${input_fasta}' |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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16 --input-dataset db/ |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
changeset
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17 #if $adv.advanced_options == 'yes' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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changeset
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18 #if $adv.input_qc_config |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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19 --input-qc-config '$adv.input_qc_config' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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20 #end if |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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21 #if $adv.input_root_seq |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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22 --input-root-seq '$adv.input_root_seq' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
diff
changeset
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23 #end if |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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24 #if $adv.input_tree |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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25 --input-tree '$adv.input_tree' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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26 #end if |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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27 #if $adv.input_gene_map |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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28 --input-gene-map '$adv.input_gene_map' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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29 #end if |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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30 #if $adv.input_pcr_primers |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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31 --input-pcr-primers '$adv.input_pcr_primers' |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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32 #end if |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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33 #if $adv.input_virus_properties |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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34 --input-virus-properties '$adv.input_virus_properties' |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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35 #end if |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
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36 #end if |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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37 #if $outputs and "report_tsv" in $outputs |
2
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
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38 #if $include_header |
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
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changeset
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39 --output-tsv '$report_tsv' |
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
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40 #else |
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
diff
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41 --output-tsv report.tsv |
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
diff
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42 #end if |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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43 #end if |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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44 #if $outputs and "report_json" in $outputs |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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45 --output-json '${report_json}' |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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46 #end if |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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47 #if $outputs and "output_tree" in $outputs |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
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48 --output-tree '${output_tree}' |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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49 #end if |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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50 #if $outputs and "output_fasta" in $outputs |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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51 --output-fasta "${output_fasta}" |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
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52 #if str($adv.advanced_options) == "yes" |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
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53 $adv.include_reference |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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54 #end if |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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55 #end if |
2
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
1
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56 #if $outputs and "report_tsv" in $outputs and not $include_header |
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
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57 && tail -n+2 report.tsv >'$report_tsv' |
1
0f20ed06ed6c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents:
0
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58 #end if |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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59 ]]></command> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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60 <inputs> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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61 <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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62 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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63 <option value="report_json">JSON format report</option> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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64 <option value="report_tsv" selected="true">Tabular format report</option> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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65 <option value="output_tree">Auspice v2 tree file (JSON format)</option> |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
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66 <option value="output_fasta">Aligned sequences (FASTA format)</option> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
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67 </param> |
2
6cd62b6d2b5c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
iuc
parents:
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68 <param name="include_header" type="boolean" label="Include header line in output file" |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
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69 truevalue="true" falsevalue="false" /> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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70 <param name="organism" type="select" label="Organism"> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
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71 <option value="sars-cov-2" selected="true">SARS-CoV-2</option> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
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72 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
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73 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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74 <option value="flu_vic_ha">Influenza B Victoria HA</option> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
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75 <option value="flu_yam_ha">Influenza B Yamagata HA</option> |
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
changeset
|
76 </param> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
77 <conditional name="adv"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
78 <param name="advanced_options" type="select" label="Use advanced options" > |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
79 <option value="yes">Yes</option> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
80 <option value="no" selected="true">No</option> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
81 </param> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
82 <when value="yes"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
83 <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
84 <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
85 <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
86 <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
87 <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" /> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
changeset
|
88 <param argument="--input-virus-properties" name="input_virus_properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation." /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
changeset
|
89 <param argument="--include-reference" name="include_reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
90 </when> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
91 <when value="no"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
92 </when> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
93 </conditional> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
94 </inputs> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
95 <outputs> |
1
0f20ed06ed6c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents:
0
diff
changeset
|
96 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
97 <filter>outputs and "report_tsv" in outputs</filter> |
1
0f20ed06ed6c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents:
0
diff
changeset
|
98 <actions> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
changeset
|
99 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" /> |
1
0f20ed06ed6c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
iuc
parents:
0
diff
changeset
|
100 </actions> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
101 </data> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
102 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
103 <filter>outputs and "report_json" in outputs</filter> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
104 </data> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
105 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
106 <filter>outputs and "output_tree" in outputs</filter> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
107 </data> |
4
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
diff
changeset
|
108 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)"> |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
diff
changeset
|
109 <filter>outputs and "output_fasta" in outputs</filter> |
b74b9a7b3e3b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
iuc
parents:
3
diff
changeset
|
110 </data> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
111 </outputs> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
112 <tests> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
113 <test expect_num_outputs="1"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
114 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
115 <param name="outputs" value="report_tsv" /> |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
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|
116 <param name="organism" value="sars-cov-2" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
117 <output name="report_tsv"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
118 <assert_contents> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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|
119 <has_n_columns n="62" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
120 <has_text text="20A" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
121 </assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
122 </output> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
123 </test> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
124 <test expect_num_outputs="3"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
125 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
126 <param name="outputs" value="report_tsv,report_json,output_tree" /> |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
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|
127 <param name="organism" value="sars-cov-2" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
128 <output name="report_tsv"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
129 <assert_contents> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents:
8
diff
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|
130 <has_n_columns n="62" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
131 <has_text text="20A" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
132 </assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
133 </output> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
134 <output name="report_json"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
135 <assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
136 <has_text text='"pos": 240,' /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
137 </assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
138 </output> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
139 <output name="output_tree"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
140 <assert_contents> |
7
f6db3ce6ed1c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
iuc
parents:
6
diff
changeset
|
141 <has_text text='"title": "QC Status"' /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
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|
142 </assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
143 </output> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
144 </test> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
145 <test expect_num_outputs="1"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
146 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff
changeset
|
147 <param name="outputs" value="report_tsv" /> |
5
0c46b95d60c3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents:
4
diff
changeset
|
148 <param name="organism" value="sars-cov-2" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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149 <conditional name="adv"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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150 <param name="advanced_options" value="yes" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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151 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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152 </conditional> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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153 <output name="report_tsv"> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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154 <assert_contents> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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155 <has_n_columns n="62" /> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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156 <has_text text="mediocre" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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157 </assert_contents> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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158 </output> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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159 </test> |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
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160 <test expect_num_outputs="2"> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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161 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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162 <param name="outputs" value="report_tsv,output_fasta" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
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163 <param name="organism" value="sars-cov-2" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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164 <conditional name="adv"> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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165 <param name="advanced_options" value="yes" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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166 <param name="include_reference" value="true" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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167 </conditional> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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168 <output name="report_tsv"> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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169 <assert_contents> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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170 <has_n_columns n="62" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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171 <has_text text="mediocre" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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172 </assert_contents> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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173 </output> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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174 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" /> |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
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175 </test> |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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176 </tests> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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177 <help><![CDATA[ |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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178 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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179 .. class:: infomark |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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180 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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181 **What it does** |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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182 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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183 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes. |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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184 |
13
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
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185 For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_. |
64be7ff9b97b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
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186 |
0
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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187 **Input** |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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188 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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189 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes. |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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190 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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191 **Output** |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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192 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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193 Outputs can include: |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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194 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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195 * A tabular format file with a report, one line per input sequence |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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196 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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197 * A JSON format file with the same information as is present in the tabular report |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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198 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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199 * An Auspice v2 tree file in JSON format |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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200 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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201 .. _Nextclade: https://github.com/nextstrain/nextclade |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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202 |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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203 ]]></help> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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204 <expand macro="citations" /> |
615f484bdb4a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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205 </tool> |