Mercurial > repos > iuc > stacks2_kmerfilter
annotate stacks_kmerfilter.xml @ 1:38c9f9a680f0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author | iuc |
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date | Mon, 30 Sep 2019 14:18:47 -0400 |
parents | b2e3553e1be2 |
children | 8a55d29c8fcf |
rev | line source |
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0
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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1 <tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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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
iuc
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3 <macros> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
parents:
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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
iuc
parents:
diff
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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
iuc
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9 @FASTQ_INPUT_FUNCTIONS@ |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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10 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
iuc
parents:
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12 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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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
iuc
parents:
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14 $link_command |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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15 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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16 kmer_filter |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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17 #if $input_type.input_type_select == 'single': |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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18 -f '$fwd_path' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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19 #else |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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20 -1 '$fwd_path' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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21 -2 '$rev_path' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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22 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
iuc
parents:
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changeset
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24 -i $inputype |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
iuc
parents:
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26 $capture |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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27 -y fastq |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
iuc
parents:
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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
parents:
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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
iuc
parents:
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31 --max_k_freq $options_advanced_filtering.max_k_freq |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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32 #if str($options_advanced_filtering.min_lim)!="": |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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33 --min_lim $options_advanced_filtering.min_lim |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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34 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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35 #if str($options_advanced_filtering.max_lim)!="": |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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36 --max_lim $options_advanced_filtering.max_lim |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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37 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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38 #if str($options_normalization.normalize)!="": |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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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
parents:
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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
parents:
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41 #if $options_kmer_char.write_k_freq |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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42 --read_k_freq $kfreq |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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43 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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44 $options_kmer_char.k_dist |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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45 #if $options_kmer_char.k_dist |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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46 | sed 's/KmerFrequency/# KmerFrequency/' > $kfreqdist |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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47 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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48 @TEE_APPEND_LOG@ |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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49 @CAT_LOG_TO_STDERR@ |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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50 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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51 ## move outputs such that Galaxy can find them |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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52 ## if filtering is on then ...filt...fq is created |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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53 ## if normalization is on then ...norm...fq is created |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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54 ## if both are active then both files are created, but only norm is needed |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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55 #if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="": |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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56 #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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57 #set infix="norm" |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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58 #else |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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59 #set infix="fil" |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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60 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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61 #if $capture: |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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62 #if $input_type.input_type_select == "single" |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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63 && mv stacks_outputs/*.discards.fastq '$discarded' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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64 #else |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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65 && mv stacks_outputs/*.1.discards.fastq '$discarded_pair.forward' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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66 && mv stacks_outputs/*.2.discards.fastq '$discarded_pair.reverse' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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67 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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68 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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69 #if $input_type.input_type_select == "single" |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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70 && mv stacks_outputs/*.${infix}.fastq '$clean' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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71 #else |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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72 && mv stacks_outputs/*.1.${infix}.fastq '$clean_pair.forward' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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73 && mv stacks_outputs/*.2.${infix}.fastq '$clean_pair.reverse' |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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74 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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75 #end if |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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76 |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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77 ]]></command> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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78 <inputs> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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79 <expand macro="fastq_input_bc"/> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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80 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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81 <section name="options_filtering" title="Filtering options" expanded="False"> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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82 <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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83 <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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84 <param argument="--k_len" type="integer" value="15" label="K-mer size" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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85 </section> |
b2e3553e1be2
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86 <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False"> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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87 <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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88 <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)." /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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89 <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)" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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90 </section> |
b2e3553e1be2
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91 <section name="options_normalization" title="Normalization options" expanded="False"> |
b2e3553e1be2
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92 <param argument="--normalize" type="integer" value="" optional="true" label="Normalize read depth according to k-mer coverage" /> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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93 </section> |
b2e3553e1be2
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94 <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False"> |
b2e3553e1be2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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95 <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" /> |
b2e3553e1be2
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96 <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="Print k-mer frequency distribution and exit" /> |
b2e3553e1be2
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97 </section> |
b2e3553e1be2
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98 <!--<section name="options_advanced_input" title="Advanced input options" expanded="False"> |
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99 <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" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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100 </section>--> |
b2e3553e1be2
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101 <expand macro="in_log"/> |
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102 </inputs> |
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103 <outputs> |
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104 <expand macro="out_log"/> |
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105 <data name="clean" format="fastqsanger" label="${tool.name} on ${on_string}"> |
b2e3553e1be2
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106 <filter>input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter> |
b2e3553e1be2
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107 </data> |
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108 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}"> |
b2e3553e1be2
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109 <filter>input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter> |
b2e3553e1be2
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110 </collection> |
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111 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads"> |
b2e3553e1be2
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112 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter> |
b2e3553e1be2
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113 </data> |
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114 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads"> |
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115 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter> |
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116 </collection> |
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117 <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies"> |
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118 <filter>options_kmer_char['write_k_freq']</filter> |
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119 </data> |
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120 <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution"> |
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121 <filter>options_kmer_char['k_dist']</filter> |
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122 </data> |
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123 </outputs> |
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124 <tests> |
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125 <!-- default output for filtering --> |
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126 <test> |
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127 <conditional name="input_type"> |
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128 <param name="input_type_select" value="single" /> |
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129 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> |
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130 </conditional> |
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131 <param name="add_log" value="yes" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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132 <output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/> |
0
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133 <param name="rare" value="--rare"/> |
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134 <param name="abundant" value="--abundant" /> |
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135 <param name="k_len" value="16" /> |
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136 <assert_command> |
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137 <has_text text="--rare" /> |
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138 <has_text text="--abundant" /> |
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139 <has_text text="--k_len 16" /> |
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140 </assert_command> |
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141 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> |
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142 </test> |
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143 <test> |
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144 <conditional name="input_type"> |
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145 <param name="input_type_select" value="paired" /> |
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146 <param name="fqinputs"> |
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147 <collection type="paired"> |
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148 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> |
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149 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> |
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150 </collection> |
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151 </param> |
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152 </conditional> |
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153 <param name="capture" value="-D" /> |
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154 <param name="normalize" value="1" /> |
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155 <assert_command> |
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156 <has_text text="--normalize 1" /> |
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157 </assert_command> |
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158 <output_collection name="clean_pair" type="paired"> |
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159 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> |
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160 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> |
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161 </output_collection> |
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162 <output_collection name="discarded_pair" type="paired"> |
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163 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> |
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164 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> |
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165 </output_collection> |
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166 </test> |
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167 <!-- kfreq output --> |
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168 <test> |
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169 <conditional name="input_type"> |
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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" /> |
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172 </conditional> |
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173 <section name="options_kmer_char"> |
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174 <param name="write_k_freq" value="--write_k_freq" /> |
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175 </section> |
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176 <output name="kfreq" file="kmerfilter/kfreq.tsv"/> |
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177 </test> |
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178 <!-- kfreqdist output --> |
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179 <test> |
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180 <conditional name="input_type"> |
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181 <param name="input_type_select" value="single" /> |
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182 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> |
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183 </conditional> |
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184 <section name="options_kmer_char"> |
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185 <param name="k_dist" value="--k_dist" /> |
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186 </section> |
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187 <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/> |
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188 </test> |
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189 </tests> |
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190 <help> |
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191 <![CDATA[ |
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192 .. class:: infomark |
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193 |
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194 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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195 |
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196 @STACKS_INFOS@ |
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197 ]]> |
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198 </help> |
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199 <expand macro="citation" /> |
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200 </tool> |