Mercurial > repos > bgruening > fastq_info

annotate fastq_info.xml @ 0:7a821cd57b43 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
author bgruening
date Sun, 12 Sep 2021 19:28:19 +0000
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0
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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1 <tool id="fastq_info" name="FASTQ info" version="@TOOL_VERSION@+Galaxy@SUFFIX_VERSION@" profile="20.01">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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2 <description>validates single or paired fastq files</description>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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3 <macros>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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4 <import>macros.xml</import>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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5 </macros>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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6 <expand macro="edam_ontology"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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7 <expand macro="requirements"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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8 <command detect_errors="exit_code"><![CDATA[
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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9 fastq_info
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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10 #if $input_option.input_type == 'single'
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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11 $input_option.fastq_1
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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12 #else
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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13 $input_option.fastq_1
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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14 $input_option.fastq_2
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15 #end if
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16 $r
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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17 $q
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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18 2>&1 | tee ./output.txt
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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19 ]]> </command>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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20 <inputs>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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21 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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22 <param name="input_type" type="select" label="Single reads or paired reads" help="Select between paired and single end data">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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23 <option value="single">Single</option>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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24 <option value="paired">Paired</option>
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25 </param>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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26 <when value="single">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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27 <param name="fastq_1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file" help="Input FASTQ file"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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28 </when>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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29 <when value="paired">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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30 <param name="fastq_1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: forward reads"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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31 <param name="fastq_2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" label="FASTQ file: reverse reads"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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32 </when>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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33 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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34 <param argument="-q" type="boolean" truevalue="" falsevalue="-q" checked="True" label="Determine quality scoring" help="If this option is disabled, it won't fail if the quality encoding cannot be determined" />
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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35 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="False" label="Skip check for duplicated readnames" help="By using this option no checks are made to determine if the read names/identifiers are unique (it will run faster and use less memory)" />
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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36 </inputs>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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37 <outputs>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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38 <data name="output" format="txt" from_work_dir="./output.txt" label="${tool.name} on ${on_string}: Validation result">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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39 </data>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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40 </outputs>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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41 <tests>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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42 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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43 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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44 <param name="input_type" value="single"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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45 <param name="fastq_1" value="R1.fastq"/>
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46 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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47 <output name="output" file="output.txt" ftype="txt" lines_diff="2">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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48 <assert_contents>
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49 <has_text text="OK"/>
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50 <has_size value="362" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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51 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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52 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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53 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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54 <!--Test gzip files-->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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55 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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56 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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57 <param name="input_type" value="single"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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58 <param name="fastq_1" value="R1.fastq.gz"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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59 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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60 <output name="output" ftype="txt">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
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61 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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62 <has_text text="OK"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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63 <has_size value="368" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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64 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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65 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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66 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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67 <!--Test paired reads-->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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68 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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69 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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70 <param name="input_type" value="paired"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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71 <param name="fastq_1" value="R1.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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72 <param name="fastq_2" value="R2.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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73 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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74 <output name="output">
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75 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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76 <has_text text="OK"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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77 <has_size value="544" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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78 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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79 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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80 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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81 <!-- Test q option-->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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82 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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83 <param name="q" value="False"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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84 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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85 <param name="input_type" value="single"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
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diff changeset
86 <param name="fastq_1" value="R1.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
87 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
88 <output name="output">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
89 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
90 <has_text text="OK"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
91 <has_size value="362" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
92 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
93 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
94 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
95 <!-- Test duplicated id -->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
96 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
97 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
98 <param name="input_type" value="single"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
99 <param name="fastq_1" value="R1_duplicated.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
100 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
101 <output name="output">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
102 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
103 <has_text text="line 36: duplicated sequence SRR1294492.1207358/1"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
104 <has_size value="311" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
105 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
106 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
107 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
108 <!-- Test r option-->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
109 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
110 <param name="r" value="True"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
111 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
112 <param name="input_type" value="single"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
113 <param name="fastq_1" value="R1_duplicated.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
114 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
115 <output name="output">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
116 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
117 <has_text text="OK"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
118 <has_size value="193" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
119 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
120 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
121 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
122 <!-- Test truncated file 01 -->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
123 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
124 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
125 <param name="input_type" value="paired"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
126 <param name="fastq_1" value="R1_truncated.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
127 <param name="fastq_2" value="R2.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
128 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
129 <output name="output">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
130 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
131 <has_text text="line 32: file truncated"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
132 <has_size value="285" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
133 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
134 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
135 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
136 <!-- Test truncated file 02 -->
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
137 <test expect_num_outputs="1">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
138 <conditional name="input_option">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
139 <param name="input_type" value="paired"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
140 <param name="fastq_1" value="R1_truncated_entry.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
141 <param name="fastq_2" value="R2.fastq"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
142 </conditional>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
143 <output name="output">
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
144 <assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
145 <has_text text="unpaired read - SRR1294492.2047212/"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
146 <has_size value="557" delta="100"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
147 </assert_contents>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
148 </output>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
149 </test>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
150 </tests>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
151 <help><![CDATA[
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
152 .. class:: infomark
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
153
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
154 **Purpose**
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
155
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
156 FASTQ info is part of `FASTQ utils <https://github.com/nunofonseca/fastq_utils>`_, a set of Linux utilities to validate and manipulate fastq files.
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
157
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
158 ]]> </help>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
159 <expand macro="citations"/>
7a821cd57b43 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/fastq_info commit abe695da7640bbd2b22980452de7a5cf6698638b"
bgruening
parents:
diff changeset
160 </tool>