Mercurial > repos > iuc > stacks_assembleperead
annotate stacks_assembleperead.xml @ 11:0c741f364d18 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
author | iuc |
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date | Sun, 19 Jan 2020 06:37:54 -0500 |
parents | e6919d8ae34d |
children | 6eaf0f9836c8 |
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11
0c741f364d18
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
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1 <tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.1"> |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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2 <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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4 <import>macros.xml</import> |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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5 </macros> |
11
0c741f364d18
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
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6 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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7 <expand macro="stdio"/> |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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8 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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9 |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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10 mkdir stacks_inputs reads stacks_outputs |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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11 && |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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12 #for $input_file in $stacks_col |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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13 #set $ext = "" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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14 #if not str($input_file.element_identifier).endswith('.tsv') |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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15 #set $ext = ".tsv" |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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16 #end if |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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17 ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' && |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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18 #end for |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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19 |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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20 #for $input_file in $reads |
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ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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21 #set $name = str($input_file.element_identifier) |
ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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22 ## sort_read_pairs is expecting strange fastq names: <sample_name>.fq_2 |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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23 #if $name.endswith('.1.fq') |
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ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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24 ## handle a common case |
ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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25 #set $name = $name[:-5]+".fq_1" |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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26 #else if $name.endswith('.2.fq') |
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ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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27 ## handle a common case |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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28 #set $name = $name[:-5]+".fq_2" |
8
e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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29 #else if not $name.endswith('.fq') and not $name.endswith('.fq_2') |
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ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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30 ## no extension, consider it's a fq_2 file |
ee52d9cfaffc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
iuc
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31 #set $name = $name + ".fq_2" |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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32 #end if |
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e6919d8ae34d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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33 ln -s '${input_file}' 'reads/${name}' && |
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e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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34 #end for |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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35 |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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36 sort_read_pairs.pl |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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37 -p stacks_inputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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38 -s 'reads' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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39 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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40 #if $whitelist |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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41 -w '$whitelist' |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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42 #end if |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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43 |
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44 #if $threshold |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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45 -r $threshold |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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46 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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47 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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48 -o stacks_outputs |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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49 |
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50 #if $velvet.use_velvet == "yes" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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51 ## remove possible empty files |
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0c741f364d18
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
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52 && find stacks_outputs -type f -size 0 -exec rm {} \; |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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53 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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54 && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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55 mkdir assembled |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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56 && |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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57 velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"` |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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58 && |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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59 exec_velvet.pl -s stacks_outputs -o assembled -c -M ${velvet.contig_length} -e "\$velvet_path" |
e3ca198820a8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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60 #end if |
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61 |
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62 ]]></command> |
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63 <inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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64 <param name="stacks_col" argument="-p" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
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65 <param name="reads" argument="-s" format="fastqsanger" type="data" multiple="true" label="Files containing reads to assemble" help="only R2 reads" /> |
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66 |
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67 <param name="whitelist" argument="-w" format="txt,tabular" type="data" optional="true" label="White list of catalog IDs to include" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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68 <param name="threshold" argument="-r" type="integer" value="" optional="true" label="Minimum number of reads by locus"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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69 |
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70 <conditional name="velvet"> |
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71 <param name="use_velvet" type="select" label="Perform assembly with Velvet" help="If not selected, the tool will only produce of collection of fasta files (one per locus) containing reads ready to assemble."> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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72 <option value="no" selected="true">No</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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73 <option value="yes">Yes</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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74 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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75 <when value="no"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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76 <when value="yes"> |
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77 <param name="contig_length" type="integer" value="200" label="Minimum length for asssembled contigs"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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78 </when> |
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79 </conditional> |
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80 </inputs> |
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81 <outputs> |
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82 <collection name="collated" type="list" label="Collated FASTA files per locus on ${on_string}"> |
8
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83 <filter>velvet['use_velvet'] == "no"</filter> |
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84 <discover_datasets pattern="(?P<name>.+)\.fa(sta)?$" ext="fasta" directory="stacks_outputs" /> |
0
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85 </collection> |
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86 |
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87 <data format="fasta" name="contigs" label="Assembled contigs on ${on_string}" from_work_dir="assembled/collated.fa"> |
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88 <filter>velvet['use_velvet'] == "yes"</filter> |
0
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89 </data> |
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90 </outputs> |
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91 |
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92 <tests> |
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93 <test> |
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94 <param name="stacks_col"> |
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95 <collection type="list"> |
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96 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> |
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97 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> |
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98 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> |
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99 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" /> |
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100 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" /> |
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101 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" /> |
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102 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" /> |
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103 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" /> |
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104 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> |
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105 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> |
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106 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> |
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107 </collection> |
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108 </param> |
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109 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> |
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110 |
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111 <output_collection name="collated"> |
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112 <element name="1"> |
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113 <assert_contents> |
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114 <has_text text="CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG" /> |
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115 </assert_contents> |
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116 </element> |
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117 </output_collection> |
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118 </test> |
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119 <test> |
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120 <param name="stacks_col"> |
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121 <collection type="list"> |
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122 <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> |
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123 <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> |
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124 <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> |
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125 <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" /> |
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126 <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" /> |
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127 <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" /> |
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128 <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" /> |
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129 <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" /> |
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130 <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> |
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131 <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> |
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132 <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> |
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133 </collection> |
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134 </param> |
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135 <param name="reads" value="demultiplexed/PopA_01.2.fq,demultiplexed/PopA_02.2.fq" ftype="fastqsanger" /> |
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136 <param name="velvet|use_velvet" value="yes" /> |
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137 <param name="velvet|contig_length" value="20" /> |
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138 |
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139 <output name="contigs"> |
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140 <assert_contents> |
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141 <has_text text="|NODE_" /> |
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142 </assert_contents> |
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143 </output> |
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144 </test> |
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145 </tests> |
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146 |
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147 <help> |
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148 <![CDATA[ |
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149 .. class:: infomark |
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150 |
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151 **What it does** |
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152 |
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153 This program will run each of the Stacks sort_read_pairs.pl and exec_velvet.pl utilities to assemble pair-end reads from STACKS pipeline results |
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154 |
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155 -------- |
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156 |
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157 **Input file** |
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158 |
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159 Output from denovo_map or ref_map |
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160 |
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161 |
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162 **Output file** |
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163 |
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164 A collated.fa file containing assembled contigs for each locus |
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165 |
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166 @STACKS_INFOS@ |
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167 ]]> |
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168 </help> |
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169 <expand macro="citation" /> |
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170 </tool> |