Mercurial > repos > iuc > dada2_plotqualityprofile

annotate dada2_plotQualityProfile.xml @ 9:81b7f9681f3c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
author iuc
date Tue, 11 Feb 2025 23:23:12 +0000
parents 2c3235c72ec1
children 1b5cec4b66ec
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9
81b7f9681f3c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit bbbc0e71b1db299a7c7296f25ac7adcccd27fbe3
iuc
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1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description>plot a visual summary of the quality scores</description>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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3 <macros>
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4 <import>macros.xml</import>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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5 </macros>
6
543d292268b9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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6 <expand macro="bio_tools"/>
0
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command detect_errors="exit_code"><![CDATA[
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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11 ##name files by linking
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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12 #import re
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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13 mkdir forward &&
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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14 #if $batch_cond.paired_cond.paired_select != "single"
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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15 mkdir reverse &&
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16 #end if
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17
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18 #if $batch_cond.batch_select == "batch":
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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19 #set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier))
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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20 #if $batch_cond.paired_cond.paired_select != "paired"
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21 ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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22 #else
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23 ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' &&
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24 ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' &&
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25 #end if
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26 #if $batch_cond.paired_cond.paired_select == "separate"
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27 ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' &&
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28 #end if
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29 #else
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30 #for $read in $batch_cond.paired_cond.reads:
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31 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
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32 #if $batch_cond.paired_cond.paired_select != "paired"
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33 ln -s '$read' forward/'$elid' &&
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34 #else
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35 ln -s '$read.forward' forward/'$elid' &&
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36 ln -s '$read.reverse' reverse/'$elid' &&
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37 #end if
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38 #end for
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39 #if $batch_cond.paired_cond.paired_select == "separate"
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40 #for $read in $batch_cond.paired_cond.sdaer:
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41 #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier))
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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42 ln -s '$read' reverse/'$elid' &&
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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43 #end for
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44 #end if
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45 #end if
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46
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47 Rscript --slave '$dada2_script'
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48 ]]></command>
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49 <configfiles>
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50 <configfile name="dada2_script"><![CDATA[
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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51 #import re
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52 library(ggplot2, quietly=T)
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53 library(dada2, quietly=T)
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54
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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55 #if $batch_cond.batch_select != "batch"
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56 agg = $batch_cond.aggregate
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57 #else
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58 agg = FALSE
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59 #end if
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60
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61 fwd_files = list.files("forward", full.names=T)
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62 qp <- plotQualityProfile(fwd_files, n=$n, aggregate = agg)
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63 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm"))
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64
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65 #if $batch_cond.paired_cond.paired_select != "single"
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66 rev_files = list.files("reverse", full.names=T)
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67 qp <- plotQualityProfile(rev_files, n=$n, aggregate = agg)
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68 ggsave('output_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
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69 #end if
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70 ]]></configfile>
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71 </configfiles>
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72 <inputs>
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73 <conditional name="batch_cond">
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74 <param name="batch_select" type="select" label="Processing mode" help="Joint processing processes all reads at once in a single job creating a single output (two in the case of paired data). Batch processes the samples in separate jobs and creates separate output for each">
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75 <option value="joint">Joint</option>
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76 <option value="batch">Batch</option>
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77 </param>
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78 <when value="joint">
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79 <expand macro="fastq_input" multiple="True" collection_type="list:paired" argument_fwd="fl" argument_rev="fl"/>
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80 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/>
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81 </when>
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82 <when value="batch">
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83 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fl" argument_rev="fl"/>
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84 </when>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
85 </conditional>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
86 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
87 </inputs>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
88 <outputs>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
89 <data name="output" format="pdf" from_work_dir="output.pdf">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
90 <filter>batch_cond['paired_cond']['paired_select'] == "single"</filter>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
91 </data>
8
2c3235c72ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
iuc
parents: 6
diff changeset
92 <data name="output_fwd" format="pdf" default_identifier_source="batch_cond|paired_cond|reads" from_work_dir="output.pdf" label="${tool.name} on ${on_string}: forward reads">
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
93 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
94 </data>
8
2c3235c72ec1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 3dd3145db6ed58efc3bf5f71e96515173967fc72
iuc
parents: 6
diff changeset
95 <data name="output_rev" format="pdf" default_identifier_source="batch_cond|paired_cond|sdaer" from_work_dir="output_rev.pdf" label="${tool.name} on ${on_string}: reverse reads">
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
96 <filter>batch_cond['paired_cond']['paired_select'] != "single"</filter>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
97 </data>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
98 </outputs>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
99 <tests>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
100 <!-- all tests are against the same file using a delta that should ensure that the pdf contains a plot -->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
101 <!-- paired joint, no-aggregate -->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
102 <test expect_num_outputs="2">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
103 <param name="batch_cond|batch_select" value="joint"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
104 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
105 <param name="batch_cond|paired_cond|reads">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
106 <collection type="list:paired">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
107 <element name="F3D0_S188_L001">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
108 <collection type="paired">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
109 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
110 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
111 </collection>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
112 </element>
2
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
113 <element name="F3D141_S207_L001">
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
114 <collection type="paired">
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
115 <element name="forward" value="F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
116 <element name="reverse" value="F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
117 </collection>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
118 </element>
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
119 </collection>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
120 </param>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
121 <param name="batch_cond|aggregate" value="FALSE"/>
2
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
122 <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
123 <output name="output_rev" value="qualityProfile_rev.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
124 </test>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
125 <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) -->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
126 <test expect_num_outputs="2">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
127 <param name="batch_cond|batch_select" value="joint"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
128 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
2
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
129 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
130 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
131 <param name="batch_cond|aggregate" value="FALSE"/>
2
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
132 <output name="output_fwd" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
133 <output name="output_rev" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
134 </test>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
135 <!-- single, non-batch, aggregate, small sample -->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
136 <test expect_num_outputs="1">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
137 <param name="batch_cond|batch_select" value="joint"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
138 <param name="batch_cond|paired_cond|paired_select" value="single"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
139 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
140 <param name="n" value="10000"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
141 <param name="batch_cond|aggregate" value="TRUE"/>
2
73c03d6288f1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents: 0
diff changeset
142 <output name="output" value="qualityProfile_fwd.pdf" ftype="pdf" compare="sim_size" delta="16000"/>
0
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
143 </test>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
144
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
145 <!-- paired, batch -->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
146 <test expect_num_outputs="2">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
147 <param name="batch_cond|batch_select" value="batch"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
148 <param name="batch_cond|paired_cond|paired_select" value="paired"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
149 <param name="batch_cond|paired_cond|reads">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
150 <collection type="paired">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
151 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
152 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
153 </collection>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
154 </param>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
155 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
156 <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
157 </test>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
158 <!-- paired-separate batch (sim_size because element ids differ)-->
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
159 <test expect_num_outputs="2">
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
160 <param name="batch_cond|batch_select" value="batch"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
161 <param name="batch_cond|paired_cond|paired_select" value="separate"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
162 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff changeset
163 <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
944958061b0f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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164 <output name="output_fwd" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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165 <output name="output_rev" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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166 </test>
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167 <!-- single, batch -->
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168 <test expect_num_outputs="1">
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169 <param name="batch_cond|batch_select" value="batch"/>
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170 <param name="batch_cond|paired_cond|paired_select" value="single"/>
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171 <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
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172 <param name="n" value="10000"/>
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173 <output name="output" value="qualityProfile.pdf" ftype="pdf" compare="sim_size" delta="15000"/>
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174 </test>
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175 </tests>
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176 <help><![CDATA[
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177 Summary
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178 .......
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179
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180 This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq datasets.
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181
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182 Details
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183 .......
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184
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185 The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles. If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend
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186 to at least that position.
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187
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188 @HELP_OVERVIEW@
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189 ]]></help>
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190 <expand macro="citations"/>
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191 </tool>