Mercurial > repos > iuc > stacks_procrad
annotate stacks_procrad.xml @ 10:8fe258d72ff3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 689ccfe1532a4de7b60fe69cd3945601d76aefb6"
author | iuc |
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date | Thu, 26 Sep 2019 10:23:32 -0400 |
parents | 57910d476be9 |
children | be78e39d56b3 |
rev | line source |
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4
c2733bcc51f7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
iuc
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1 <tool id="stacks_procrad" name="Stacks: process radtags" version="@WRAPPER_VERSION@.0"> |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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2 <description>the Stacks demultiplexing script</description> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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3 <macros> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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4 <import>macros.xml</import> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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5 </macros> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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6 <expand macro="requirements"/> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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7 <expand macro="stdio"/> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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8 <command><![CDATA[ |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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9 |
8
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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10 #if $input_type.options_type_selector == "single" |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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11 |
8
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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12 #if $input_type.input_single.is_of_type('fastqsanger') |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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13 #set $ext = ".fq" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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14 #set inputype = "fastq" |
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bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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15 #else |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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16 #set $ext = ".fq.gz" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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17 #set inputype = "gzfastq" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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18 #end if |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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19 |
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bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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20 ln -s '$input_type.input_single' R1$ext && |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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21 #else |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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22 |
8
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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23 #if $input_type.inputs_paired1.is_of_type('fastqsanger') |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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24 #set $ext = ".fq" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff
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25 #set inputype = "fastq" |
8
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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26 #else |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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27 #set $ext = ".fq.gz" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff
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28 #set inputype = "gzfastq" |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
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29 #end if |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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30 |
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bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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31 ln -s '$input_type.inputs_paired1' R1$ext && |
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
parents:
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32 ln -s '$input_type.inputs_paired2' R2$ext && |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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33 #end if |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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34 |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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35 mkdir stacks_outputs |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
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36 |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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37 && |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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38 |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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39 process_radtags |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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40 |
8
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
iuc
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41 #if $input_type.options_type_selector == "single" |
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6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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42 -f R1$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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43 #else |
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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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44 -1 R1$ext |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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45 -2 R2$ext |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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46 #end if |
6f9e8593e571
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 -i $inputype |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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49 -b '$barcode' |
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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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50 |
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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 $input_type.barcode_encoding |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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52 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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53 #if str( $options_enzyme.options_enzyme_selector ) == "1" |
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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 -e $options_enzyme.enzyme |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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55 #else |
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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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56 --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2 |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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57 #end if |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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58 |
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59 #if str( $outype ) != "auto" |
bec1f08cdfcc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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60 -y $outype |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
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61 #end if |
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62 |
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63 $capture |
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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 |
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2837e6ae4e18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78
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65 $options_advanced.retain_header |
2837e6ae4e18
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 106c21592d6d70bfe699570394308ee6d2538d78
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66 |
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67 #if str($options_advanced.truncate) |
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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 -t $options_advanced.truncate |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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69 #end if |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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70 |
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71 -w $options_advanced.sliding |
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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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72 |
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73 $options_advanced.remove |
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74 |
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75 $options_advanced.discard |
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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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76 -s $options_advanced.score |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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77 |
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78 $options_advanced.rescue |
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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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79 |
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80 -o stacks_outputs |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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81 ]]></command> |
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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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82 |
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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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83 <inputs> |
6f9e8593e571
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
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84 <conditional name="input_type"> |
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85 <param name="options_type_selector" type="select" label="Single-end or paired-end reads files"> |
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86 <option value="single" selected="True">Single-end files</option> |
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87 <option value="paired">Paired-end files</option> |
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88 </param> |
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89 <when value="single"> |
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90 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> |
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91 |
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92 <param name="barcode_encoding" type="select" label="Barcode location"> |
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93 <expand macro="barcode_encoding_single" /> |
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94 </param> |
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95 </when> |
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96 <when value="paired"> |
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97 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> |
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98 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> |
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99 |
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100 <param name="barcode_encoding" type="select" label="Barcode location"> |
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101 <expand macro="barcode_encoding_pair" /> |
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102 </param> |
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103 </when> |
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104 </conditional> |
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105 |
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106 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" /> |
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107 |
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108 <conditional name="options_enzyme"> |
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109 <param name="options_enzyme_selector" type="select" label="Number of enzymes"> |
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110 <option value="1">One</option> |
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111 <option value="2">Two</option> |
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112 </param> |
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113 <when value="1"> |
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114 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" > |
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115 <expand macro="enzymes"/> |
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116 </param> |
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117 </when> |
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118 <when value="2"> |
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119 <param name="enzyme" type="select" label="Enzyme" argument="--renz_1" help="provide the restriction enzyme used" > |
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120 <expand macro="enzymes"/> |
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121 </param> |
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122 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" > |
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123 <expand macro="enzymes"/> |
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124 </param> |
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125 </when> |
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126 </conditional> |
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127 |
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128 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> |
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129 |
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130 <section name="options_advanced" title="advanced options" expanded="False"> |
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131 <param name="sliding" type="float" value="0.15" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15)" /> |
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132 <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> |
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133 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> |
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134 <param name="score" type="integer" value="10" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10)" /> |
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135 <param name="rescue" type="boolean" checked="false" truevalue="-r" falsevalue="" argument="-r" label="Rescue barcodes and RAD-Tags?"/> |
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136 <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> |
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137 <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> |
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138 </section> |
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139 |
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140 <param name="outype" argument="-y" type="select" label="Output format" > |
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141 <option value="auto" selected="True">Same as input</option> |
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142 <option value="fastq">fastq</option> |
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143 <option value="fasta">fasta</option> |
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144 <option value="gzfastq">gzipped fastq</option> |
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145 </param> |
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146 </inputs> |
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147 |
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148 <outputs> |
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149 <data format="txt" name="output_log" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" from_work_dir="stacks_outputs/process_radtags.log" /> |
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150 |
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151 <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> |
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152 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> |
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153 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> |
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154 <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> |
0
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155 </collection> |
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156 <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> |
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157 <filter>input_type['options_type_selector'] == "paired"</filter> |
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158 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> |
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159 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> |
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160 <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> |
0
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161 </collection> |
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162 <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> |
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163 <filter>capture is True</filter> |
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164 <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" /> |
8
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165 <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped --> |
3
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166 <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" /> |
0
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167 </collection> |
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168 </outputs> |
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169 |
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170 <tests> |
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171 <test> |
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172 <param name="options_type_selector" value="single"/> |
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173 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/> |
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174 <param name="barcode" value="procrad/barcodes"/> |
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175 <param name="options_enzyme_selector" value="1"/> |
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176 <param name="enzyme" value="ecoRI"/> |
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177 <param name="discard" value="true"/> |
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178 <param name="capture" value="true"/> |
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179 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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180 <output_collection name="demultiplexed"> |
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181 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/> |
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182 </output_collection> |
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183 <output_collection name="discarded"> |
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184 <element name="R1"> |
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185 <assert_contents> |
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186 <has_text text="lane1_fakedata0_11" /> |
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187 </assert_contents> |
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188 </element> |
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189 </output_collection> |
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190 </test> |
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191 <test> |
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192 <param name="options_type_selector" value="single"/> |
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193 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/> |
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194 <param name="barcode" value="procrad/barcodes"/> |
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195 <param name="options_enzyme_selector" value="1"/> |
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196 <param name="enzyme" value="ecoRI"/> |
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197 <param name="discard" value="true"/> |
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198 <param name="capture" value="true"/> |
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199 <param name="outype" value="gzfastq"/> |
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200 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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201 <output_collection name="demultiplexed"> |
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202 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> |
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203 </output_collection> |
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204 <output_collection name="discarded"> |
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205 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> |
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206 </output_collection> |
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207 </test> |
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208 <test> |
0
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209 <param name="options_type_selector" value="paired"/> |
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210 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> |
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211 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> |
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212 <param name="barcode" value="procrad/barcodes"/> |
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213 <param name="options_enzyme_selector" value="1"/> |
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214 <param name="enzyme" value="ecoRI"/> |
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215 <param name="discard" value="true"/> |
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216 <param name="capture" value="true"/> |
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217 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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218 <output_collection name="demultiplexed"> |
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219 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/> |
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220 </output_collection> |
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221 <output_collection name="remaining"> |
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222 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/> |
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223 </output_collection> |
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224 <output_collection name="discarded"> |
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225 <element name="R1"> |
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226 <assert_contents> |
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227 <has_text text="lane1_fakedata0_11" /> |
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228 </assert_contents> |
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229 </element> |
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230 </output_collection> |
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231 </test> |
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232 <test> |
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233 <param name="options_type_selector" value="paired"/> |
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234 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> |
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235 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> |
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236 <param name="barcode" value="procrad/barcodes"/> |
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237 <param name="options_enzyme_selector" value="1"/> |
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238 <param name="enzyme" value="ecoRI"/> |
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239 <param name="discard" value="true"/> |
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240 <param name="capture" value="true"/> |
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241 <param name="retain_header" value="true"/> |
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242 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
2837e6ae4e18
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243 <output_collection name="demultiplexed"> |
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244 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fq.header"/> |
2837e6ae4e18
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245 </output_collection> |
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246 <output_collection name="remaining"> |
2837e6ae4e18
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247 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fq"/> |
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248 </output_collection> |
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249 <output_collection name="discarded"> |
2837e6ae4e18
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250 <element name="R1"> |
2837e6ae4e18
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251 <assert_contents> |
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252 <has_text text="lane1_fakedata0_11" /> |
2837e6ae4e18
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253 </assert_contents> |
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254 </element> |
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255 </output_collection> |
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256 </test> |
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257 <test> |
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258 <param name="options_type_selector" value="paired"/> |
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259 <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> |
2837e6ae4e18
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260 <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> |
2837e6ae4e18
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261 <param name="barcode" value="procrad/barcodes"/> |
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262 <param name="options_enzyme_selector" value="1"/> |
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263 <param name="enzyme" value="ecoRI"/> |
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264 <param name="discard" value="true"/> |
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265 <param name="capture" value="true"/> |
0
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266 <param name="outype" value="fasta"/> |
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267 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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268 <output_collection name="demultiplexed"> |
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269 <element name="PopA_01.1" compare="sim_size" file="demultiplexed/PopA_01.1.fa"/> |
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270 </output_collection> |
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271 <output_collection name="remaining"> |
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272 <element name="PopA_01.rem.1" compare="sim_size" file="demultiplexed/PopA_01.rem.1.fa"/> |
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273 </output_collection> |
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274 <output_collection name="discarded"> |
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275 <element name="R1"> |
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276 <assert_contents> |
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277 <has_text text="lane1_fakedata0_11" /> |
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278 </assert_contents> |
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279 </element> |
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280 </output_collection> |
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281 </test> |
8
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282 <test> |
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283 <param name="options_type_selector" value="single"/> |
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284 <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/> |
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285 <param name="barcode" value="procrad/barcodes"/> |
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286 <param name="options_enzyme_selector" value="1"/> |
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287 <param name="enzyme" value="ecoRI"/> |
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288 <param name="discard" value="true"/> |
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289 <param name="capture" value="true"/> |
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290 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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291 <output_collection name="demultiplexed"> |
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292 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/> |
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293 </output_collection> |
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294 <output_collection name="discarded"> |
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295 <element name="R1"> |
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296 <assert_contents> |
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297 <has_text text="lane1_fakedata0_11" /> |
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298 </assert_contents> |
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299 </element> |
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300 </output_collection> |
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301 </test> |
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302 <test> |
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303 <param name="options_type_selector" value="single"/> |
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304 <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/> |
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305 <param name="barcode" value="procrad/barcodes"/> |
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306 <param name="options_enzyme_selector" value="1"/> |
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307 <param name="enzyme" value="ecoRI"/> |
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308 <param name="discard" value="true"/> |
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309 <param name="capture" value="true"/> |
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310 <param name="outype" value="gzfastq"/> |
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311 <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> |
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312 <output_collection name="demultiplexed"> |
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313 <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/> |
bec1f08cdfcc
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314 </output_collection> |
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315 <output_collection name="discarded"> |
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316 <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> |
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317 </output_collection> |
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318 </test> |
0
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319 </tests> |
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320 |
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321 |
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322 |
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323 <help> |
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324 <![CDATA[ |
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325 .. class:: infomark |
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326 |
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327 **What it does** |
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328 |
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329 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but can be specified on the command line (the threshold and window size can be adjusted). |
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330 |
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331 The process_radtags program can: |
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332 |
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333 - handle data that is barcoded, either inline or using an index, or unbarcoded. |
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334 - use combinatorial barcodes. |
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335 - check and correct for a restriction enzyme cutsite for single or double-digested data. |
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336 - filter adapter sequence while allowing for sequencing error in the adapter pattern. |
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337 - process individual files or whole directories of files. |
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338 - directly read gzipped data |
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339 - filter reads based on Illumina's Chastity filter |
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340 |
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341 **Help** |
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342 |
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343 Input files: |
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344 |
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345 - FASTQ |
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346 |
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347 - Barcode File Format |
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348 |
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349 The barcode file is a very simple format: |
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350 |
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351 ======= =========== |
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352 Barcode Sample name |
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353 ======= =========== |
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354 ATGGGG PopA_01 |
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355 GGGTAA PopA_02 |
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356 AGGAAA PopA_03 |
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357 TTTAAG PopA_04 |
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358 GGTGTG PopA_05 |
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359 TGATGT PopA_06 |
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360 ======= =========== |
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361 |
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362 Combinatorial barcodes are specified, one per column, separated by a tab: |
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363 |
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364 ======== ======== =========== |
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365 Barcode1 Barcode2 Sample name |
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366 ======== ======== =========== |
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367 CGATA ACGTA PopA_01 |
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368 CGGCG CGTA PopA_02 |
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369 GAAGC CGTA PopA_03 |
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370 GAGAT CGTA PopA_04 |
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371 CGATA AGCA PopA_05 |
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372 CGGCG AGCA PopA_06 |
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373 ======== ======== =========== |
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374 |
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375 @STACKS_INFOS@ |
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376 ]]> |
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377 </help> |
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378 <expand macro="citation" /> |
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379 </tool> |