Mercurial > repos > iuc > stacks2_kmerfilter

annotate stacks_kmerfilter.xml @ 6:d30e36c48c93 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 2f4c9bfc48d63075ae18a1687e8d01ffea509084
author iuc
date Wed, 11 May 2022 06:49:11 +0000
parents 3d70c2996730
children
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3d70c2996730 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
iuc
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1 <tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>Identify PCR clones</description>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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3 <macros>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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4 <import>macros.xml</import>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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5 </macros>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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6 <expand macro="requirements"/>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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7 <expand macro="version_cmd"/>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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8 <command detect_errors="aggressive"><![CDATA[
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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9 @FASTQ_INPUT_FUNCTIONS@
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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10 trap ">&2 cat '$output_log'" err exit &&
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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11 mkdir stacks_inputs stacks_outputs &&
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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12
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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13 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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14 $link_command
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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15
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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16 kmer_filter
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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17 #if $input_type.input_type_select == 'single':
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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18 -f '$fwd_path'
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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19 #else
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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20 -1 '$fwd_path'
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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21 -2 '$rev_path'
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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22 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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23 ## TODO $options_kmer_char.read_k_freq
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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24 -i $inputype
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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25 -o stacks_outputs
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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26 $capture
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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27 -y fastq
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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28 $options_filtering.rare
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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29 $options_filtering.abundant
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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30 --k_len $options_filtering.k_len
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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31 --max_k_freq $options_advanced_filtering.max_k_freq
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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32 #if str($options_advanced_filtering.min_lim)!="":
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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33 --min_lim $options_advanced_filtering.min_lim
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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34 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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35 #if str($options_advanced_filtering.max_lim)!="":
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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36 --max_lim $options_advanced_filtering.max_lim
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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37 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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38 #if str($options_normalization.normalize)!="":
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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39 --normalize $options_normalization.normalize
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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40 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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41 #if $options_kmer_char.write_k_freq
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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42 --write-k-freq $kfreqdist
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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43 #end if
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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44 ## TODO read_k_freq
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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45 $options_kmer_char.k_dist
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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46 #if $options_kmer_char.k_dist
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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47 > '$kfreq'
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b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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48 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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49 @TEE_APPEND_LOG@
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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50
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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51 #if $options_kmer_char.k_dist
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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52 && sed -i -e 's/KmerFrequency/# KmerFrequency/' '$kfreq'
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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53 #elif $options_kmer_char.write_k_freq
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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54 && sed -i -e 's/# Kmer Count/#Kmer\tCount/; s/ /\t/' '$kfreqdist';
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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55 #else
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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56 ## move outputs such that Galaxy can find them
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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57 ## if filtering is on then ...filt...fq is created
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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58 ## if normalization is on then ...norm...fq is created
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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59 ## if both are active then both files are created, but only norm is needed
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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60 #if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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61 #if str($options_normalization.normalize)!="":
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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62 #set infix="norm"
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
iuc
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63 #else
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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64 #set infix="fil"
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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65 #end if
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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66 #if $capture:
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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67 #if $input_type.input_type_select == "single"
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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68 && mv stacks_outputs/*.discards.fastq '$discarded'
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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69 #else
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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70 && mv stacks_outputs/*.1.discards.fastq '$discarded_pair.forward'
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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71 && mv stacks_outputs/*.2.discards.fastq '$discarded_pair.reverse'
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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72 #end if
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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73 #end if
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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74 #if $input_type.input_type_select == "single"
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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75 && mv stacks_outputs/*.${infix}.fastq '$clean'
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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76 #else
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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77 && mv stacks_outputs/*.1.${infix}.fastq '$clean_pair.forward'
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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78 && mv stacks_outputs/*.2.${infix}.fastq '$clean_pair.reverse'
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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79 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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80 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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81 #end if
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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82 ]]></command>
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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83 <inputs>
5
3d70c2996730 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
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84 <expand macro="fastq_input"/>
2
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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85 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
0
b2e3553e1be2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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86 <section name="options_filtering" title="Filtering options" expanded="False">
2
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87 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers"/>
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88 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers"/>
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89 <param argument="--k_len" type="integer" value="15" label="K-mer size"/>
0
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90 </section>
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91 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">
2
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92 <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant"/>
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93 <param argument="--min_lim" type="integer" value="" optional="true" label="Number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)."/>
8a55d29c8fcf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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94 <param argument="--max_lim" type="integer" value="" optional="true" label="Number of abundant kmers required to discard a read" help="(default: 80% of the k-mers in a read)"/>
0
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95 </section>
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96 <section name="options_normalization" title="Normalization options" expanded="False">
2
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97 <param argument="--normalize" type="integer" value="" optional="true" label="Normalize read depth according to k-mer coverage"/>
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98 </section>
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99 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False">
2
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100 <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="Write kmers along with their frequency of occurrence and exit"/>
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101 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="Print k-mer frequency distribution and exit"/>
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102 </section>
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103 <!--<section name="options_advanced_input" title="Advanced input options" expanded="False">
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104 <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="Read a set of kmers along with their frequencies of occurrence instead of reading raw input files"/>
0
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105 </section>-->
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106 <expand macro="in_log"/>
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107 </inputs>
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108 <outputs>
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109 <expand macro="out_log"/>
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110 <expand macro="fastq_output_filter" format="fastq">
2
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111 <filter>not options_kmer_char['k_dist'] and not options_kmer_char['write_k_freq']</filter>
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112 </expand>
0
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113 <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
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114 <filter>options_kmer_char['k_dist']</filter>
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115 </data>
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116 <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution">
2
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117 <filter>options_kmer_char['write_k_freq']</filter>
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118 </data>
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119 </outputs>
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120 <tests>
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121 <!-- default output for filtering -->
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122 <test expect_num_outputs="2">
0
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123 <conditional name="input_type">
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124 <param name="input_type_select" value="single"/>
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125 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
0
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126 </conditional>
2
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127 <param name="add_log" value="yes"/>
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128 <output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/>
0
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129 <param name="rare" value="--rare"/>
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130 <param name="abundant" value="--abundant"/>
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131 <param name="k_len" value="16"/>
0
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132 <assert_command>
2
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133 <has_text text="--rare"/>
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134 <has_text text="--abundant"/>
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135 <has_text text="--k_len 16"/>
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136 </assert_command>
2
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137 <param name="add_log" value="yes"/>
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138 <output name="output_log"><assert_contents><has_text text="5 retained reads."/></assert_contents></output>
3
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139 <output name="clean" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq.single"/>
0
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140 </test>
2
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141 <test expect_num_outputs="7">
0
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142 <conditional name="input_type">
2
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143 <param name="input_type_select" value="paired"/>
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144 <param name="fqinputs">
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145 <collection type="paired">
2
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146 <element name="forward" value="clonefilter/R1_0001.1.fq.gz"/>
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147 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz"/>
0
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148 </collection>
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149 </param>
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150 </conditional>
2
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151 <param name="capture" value="-D"/>
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152 <param name="normalize" value="1"/>
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153 <assert_command>
2
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154 <has_text text="--normalize 1"/>
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155 </assert_command>
2
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156 <param name="add_log" value="yes"/>
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157 <output name="output_log"><assert_contents><has_text text="8 retained reads."/></assert_contents></output>
0
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158 <output_collection name="clean_pair" type="paired">
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159 <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq"/>
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160 <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Removed2_0001.2.2.fq"/>
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161 </output_collection>
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162 <output_collection name="discarded_pair" type="paired">
3
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163 <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Discarded1_0001.1.1.fq"/>
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164 <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Discarded2_0001.2.2.fq"/>
0
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165 </output_collection>
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166 </test>
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167 <!-- kfreq output -->
2
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168 <test expect_num_outputs="2">
0
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169 <conditional name="input_type">
2
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170 <param name="input_type_select" value="single"/>
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171 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
0
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172 </conditional>
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173 <section name="options_kmer_char">
2
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174 <param name="write_k_freq" value="--write_k_freq"/>
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175 </section>
2
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176 <param name="add_log" value="yes"/>
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177 <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>
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178 <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>
0
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179 </test>
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180 <!-- kfreqdist output -->
2
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181 <test expect_num_outputs="1">
0
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182 <conditional name="input_type">
2
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183 <param name="input_type_select" value="single"/>
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184 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
0
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185 </conditional>
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186 <section name="options_kmer_char">
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187 <param name="k_dist" value="--k_dist"/>
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188 </section>
2
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189 <param name="add_log" value="no"/>
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190 <assert_stderr><has_text text="Generating kmer distribution..."/></assert_stderr>
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191 <output name="kfreq" file="kmerfilter/kfreq.tsv"/>
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192 </test>
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193 </tests>
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194 <help>
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195 <![CDATA[
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196 .. class:: infomark
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197
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198 Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.
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199
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200 @STACKS_INFOS@
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201 ]]>
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202 </help>
2
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203 <expand macro="citation"/>
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204 </tool>