Mercurial > repos > iuc > stacks2_procrad

annotate stacks_procrad.xml @ 1:56f6477cf37b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 14:13:17 -0400
parents 3d413e8cb277
children bdd7e518c7d0
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3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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1 <tool id="stacks2_procrad" name="Stacks2: process radtags" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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2 <description>the Stacks demultiplexing script</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>macros_process.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="version_cmd"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @FASTQ_INPUT_FUNCTIONS@
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11 mkdir stacks_inputs stacks_outputs &&
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12
1
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13 #if $output_log
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14 ln -s '$output_log' stacks_outputs/process_radtags.stacks_inputs.log &&
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15 #end if
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0
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17 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
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18 $link_command
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20 process_radtags
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22 @PROCESS_IOOPTIONS@
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23 @PROCESS_FILTER@
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24 @COMMON_ADVANCED@
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25 @RESCUE_BARCODE@
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26 @PROCESS_ADAPTER@
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27
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28 ## -E not implemented in Galaxy defaults to phred33
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30 ## Restriction enzyme options
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31 #if str($options_enzyme.enzyme) != '':
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32 -e $options_enzyme.enzyme
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33 #end if
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34 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='':
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35 --renz_2 $options_enzyme.enzyme2
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36 #end if
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37
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38 ## advanced options not shared between shortreads and radtags
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39 $options_advanced.bestrad
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40 $options_advanced.disable_rad_check
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41
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42 ## Output options
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43 ## --merge not implemented in Galaxy
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44
0
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45 @PROCESS_FASTQ_POSTPROC@
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46 ]]></command>
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47
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48 <inputs>
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49 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
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50 <conditional name="options_enzyme">
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51 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
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52 <option value="1">One</option>
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53 <option value="2">Two</option>
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54 </param>
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55 <when value="1">
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56 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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57 <expand macro="enzymes"/>
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58 </param>
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59 </when>
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60 <when value="2">
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61 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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62 <expand macro="enzymes"/>
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63 </param>
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64 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
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65 <expand macro="enzymes"/>
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66 </param>
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67 </when>
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68 </conditional>
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69
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70 <section name="options_advanced" title="advanced options" expanded="False">
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71 <expand macro="common_advanced"/>
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72 <param argument="--bestrad" type="boolean" checked="false" truevalue="--bestrad" falsevalue="" label="Library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads" />
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73 <param argument="--disable_rad_check" type="boolean" checked="false" truevalue="--disable_rad_check" falsevalue="" label="Disable checking if the RAD site is intact" />
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74 <expand macro="rescue_barcode"/>
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75 <expand macro="process_adapter"/>
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76 </section>
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77
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78 <expand macro="process_filter"/>
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79 <expand macro="process_output_types"/>
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80 <expand macro="in_log"/>
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81 </inputs>
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82
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83 <outputs>
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84 <expand macro="out_log"/>
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85 <expand macro="process_outputs"/>
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86 </outputs>
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87 <tests>
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88 <!-- single single ended input, no filtering (hence no capturing) + log -->
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89 <test>
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90 <param name="input_type|input_type_select" value="single"/>
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91 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
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92 <param name="input_type|barcode_encoding" value="--inline_null"/>
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93 <param name="barcode" value="procrad/barcodes"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
94 <param name="options_enzyme|options_enzyme_selector" value="1"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
95 <param name="options_enzyme|enzyme" value="ecoRI"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
96 <param name="add_log" value="yes" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
97 <output name="output_log" file="procrad/process_radtags.out" lines_diff="4"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
98 <output_collection name="demultiplexed" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 <element name="PopA_01" file="demultiplexed/PopA_01.fq" ftype="fastqsanger" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
101 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
102 <!-- multiple (zipped) single end input (misusing R2 as add single end read file),
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
103 discarding by quality and capturing them -->
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
104 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
105 <param name="input_type|input_type_select" value="single"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
106 <param name="input_type|fqinputs" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip,procrad/R2.fq.gzip"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
107 <param name="input_type|barcode_encoding" value="--inline_null"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
108 <param name="barcode" value="procrad/barcodes"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
109 <param name="options_enzyme|options_enzyme_selector" value="1"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
110 <param name="options_enzyme|enzyme" value="ecoRI"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
111 <param name="filter_cond|filter_select" value="yes"/>
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
112 <param name="filter_cond|discard" value="-q"/>
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
113 <param name="filter_cond|sliding" value="0.1" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
114 <param name="filter_cond|score" value="11" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
115 <param name="filter_cond|remove" value="-c" />
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
116 <param name="capture" value="-D"/>
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
117 <param name="outype" value="gzfastq"/>
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
118 <param name="add_log" value="yes" />
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
119 <output name="output_log" file="procrad/process_radtags2.out" lines_diff="4"/>
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
120 <assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
121 <has_text text="-q" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
122 <has_text text="-w 0.1" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 <has_text text="-s 11" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
124 <has_text text="-c" />
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
125 <has_text text="-D" />
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
126 </assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
127 <output_collection name="demultiplexed" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
128 <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
129 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
130 <output_collection name="discarded" count="2">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
131 <element name="R1" file="procrad/R1.fq.discards" ftype="fastqsanger"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
132 <element name="R2" file="procrad/R2.fq.discards" ftype="fastqsanger"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
133 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
135 <!-- paired input, no quality but length filter, gzfasta output -->
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
136 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
137 <param name="input_type|input_type_select" value="paired"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 <param name="input_type|fqinputs">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
139 <collection type="list:paired">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
140 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
141 <collection type="paired">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144 </collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
146 </collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
147 </param>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
148 <param name="barcode" value="procrad/barcodes"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
149 <param name="options_enzyme|options_enzyme_selector" value="1"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
150 <param name="options_enzyme|enzyme" value="ecoRI"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 <param name="filter_cond|filter_select" value="no"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
152 <param name="filter_cond|len_limit" value="50"/>
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
iuc
parents: 0
diff changeset
153 <param name="capture" value="-D"/>
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
154 <param name="outype" value="gzfasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155 <param name="add_log" value="yes" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
156 <output name="output_log" file="procrad/process_radtags_paired.out" lines_diff="4"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
157 <assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
158 <has_text text="--len_limit 50" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
159 </assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
160 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
161 <element name="PopA_01">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
162 <element name="forward" value="demultiplexed/PopA_01.1.fa.gz" ftype="fasta.gz" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 <element name="reverse" value="demultiplexed/PopA_01.2.fa.gz" ftype="fasta.gz" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
164 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
165 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
166 <output_collection name="remaining" type="list:paired" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
167 <element name="PopA_01">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
168 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa.gz" ftype="fasta.gz"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa.gz" ftype="fasta.gz"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
170 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
171 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
172 <output_collection name="discarded_paired" type="list:paired" count="1">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
173 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 <element name="forward" file="procrad/R1.fa.discards" ftype="fasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 <element name="reverse" file="procrad/R2.fa.discards" ftype="fasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
177 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
178 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
179 <!-- paired input (gzipped) + advanced options + two enzymes, fasta output -->
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
180 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
181 <param name="input_type|input_type_select" value="paired"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
182 <param name="input_type|fqinputs">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
183 <collection type="list:paired">
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184 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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185 <collection type="paired">
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iuc
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186 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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187 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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188 </collection>
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189 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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190 </collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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191 </param>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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192 <param name="barcode" value="procrad/barcodes"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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193 <param name="options_enzyme|options_enzyme_selector" value="2"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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194 <param name="options_enzyme|enzyme" value="ecoRI"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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195 <param name="options_enzyme|enzyme2" value="ecoRI"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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196 <param name="options_advanced|truncate" value="70" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
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197 <param name="options_advanced|rescue_cond|rescue" value="-r"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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198 <param name="options_advanced|rescue_cond|barcode_dist_1" value="2" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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199 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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200 <param name="options_advanced|bestrad" value="--bestrad" />
1
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201 <param name="options_advanced|retain_header" value="--retain_header"/>
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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202 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" />
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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203 <param name="options_advanced|adapter_1" value="AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" />
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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204 <param name="options_advanced|adapter_2" value="TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" />
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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205 <param name="options_advanced|adapter_mm" value="2" />
0
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206 <param name="outype" value="fasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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207 <assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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208 <has_text text="-e ecoRI" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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209 <has_text text="--renz_2 ecoRI" />
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210 <has_text text="-t 70" />
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211 <has_text text="-r" />
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212 <has_text text="--bestrad" />
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iuc
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213 <has_text text="--retain_header" />
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214 <has_text text="--disable_rad_check" />
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215 <has_text text="--barcode_dist_1 2" />
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216 <has_text text="--barcode_dist_2 2" />
1
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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217 <has_text text="--adapter_1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA" />
56f6477cf37b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
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218 <has_text text="--adapter_2 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT" />
0
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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219 <has_text text="--adapter_mm 2" />
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220 </assert_command>
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221 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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222 <element name="PopA_01">
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iuc
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223 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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224 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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225 </element>
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226 </output_collection>
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227 <output_collection name="remaining" type="list:paired" count="40">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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228 <element name="PopA_01">
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229 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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230 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" />
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231 </element>
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232 </output_collection>
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233 </test>
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234 </tests>
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235
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236 <help>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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237 <![CDATA[
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238 .. class:: infomark
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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239
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240 **What it does**
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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241
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242 This program examines raw reads from an Illumina sequencing run and first, checks that the barcode and the RAD cutsite are intact, and demultiplexes the data. If there are errors in the barcode or the RAD site within a certain allowance process_radtags can correct them. Second, it slides a window down the length of the read and checks the average quality score within the window. If the score drops below 90% probability of being correct (a raw phred score of 10), the read is discarded. This allows for some seqeuncing errors while elimating reads where the sequence is degrading as it is being sequenced. By default the sliding window is 15% of the length of the read, but the threshold and window size can be adjusted.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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243
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244 The process_radtags program can:
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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245
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246 - handle data that is barcoded, either inline or using an index, or unbarcoded.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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247 - use combinatorial barcodes.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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248 - check and correct for a restriction enzyme cutsite for single or double-digested data.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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249 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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250 - process individual files or whole directories of files.
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251 - directly read gzipped data
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252 - filter reads based on Illumina's Chastity filter
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253
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254 **Help**
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255
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256 Input files:
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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257
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258 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list)
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259
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260 - Barcode File
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261
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262 The barcode file is a very simple format:
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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263
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264 ======= ===========
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265 Barcode Sample name
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266 ======= ===========
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267 ATGGGG PopA_01
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268 GGGTAA PopA_02
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269 AGGAAA PopA_03
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270 TTTAAG PopA_04
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271 GGTGTG PopA_05
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272 TGATGT PopA_06
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273 ======= ===========
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274
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275 Combinatorial barcodes are specified, one per column, separated by a tab:
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276
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277 ======== ======== ===========
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278 Barcode1 Barcode2 Sample name
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279 ======== ======== ===========
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280 CGATA ACGTA PopA_01
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281 CGGCG CGTA PopA_02
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282 GAAGC CGTA PopA_03
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283 GAGAT CGTA PopA_04
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284 CGATA AGCA PopA_05
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285 CGGCG AGCA PopA_06
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286 ======== ======== ===========
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287
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288 The sample name column can be omitted. Then the Barcodes are used for naming the output files.
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289
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290 @STACKS_INFOS@
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291 ]]>
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292 </help>
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293 <expand macro="citation" />
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294 </tool>