Mercurial > repos > iuc > stacks2_procrad

annotate stacks_procrad.xml @ 0:3d413e8cb277 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
author iuc
date Mon, 01 Jul 2019 10:51:46 -0400
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children 56f6477cf37b
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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
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13 #set ($link_command, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
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14 $link_command
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16 process_radtags
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18 @PROCESS_IOOPTIONS@
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19 @PROCESS_FILTER@
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20 @COMMON_ADVANCED@
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21 @RESCUE_BARCODE@
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22 @PROCESS_ADAPTER@
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24 ## -E not implemented in Galaxy defaults to phred33
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25
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26 ## Restriction enzyme options
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27 #if str($options_enzyme.enzyme) != '':
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28 -e $options_enzyme.enzyme
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29 #end if
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30 #if str( $options_enzyme.options_enzyme_selector ) == "2" and str($options_enzyme.enzyme2)!='':
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31 --renz_2 $options_enzyme.enzyme2
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32 #end if
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33
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34 ## advanced options not shared between shortreads and radtags
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35 $options_advanced.bestrad
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36 $options_advanced.disable_rad_check
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37
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38 ## Output options
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39 ## --merge not implemented in Galaxy
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40 #if $output_log
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41 && mv stacks_outputs/process_radtags.stacks_inputs.log $output_log
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42 #end if
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43 @PROCESS_FASTQ_POSTPROC@
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44 ]]></command>
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45
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46 <inputs>
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47 <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
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48 <conditional name="options_enzyme">
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49 <param name="options_enzyme_selector" type="select" label="Number of enzymes">
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50 <option value="1">One</option>
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51 <option value="2">Two</option>
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52 </param>
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53 <when value="1">
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54 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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55 <expand macro="enzymes"/>
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56 </param>
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57 </when>
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58 <when value="2">
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59 <param name="enzyme" type="select" label="Enzyme" argument="-e" help="provide the restriction enzyme used" >
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60 <expand macro="enzymes"/>
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61 </param>
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62 <param name="enzyme2" type="select" label="Second enzyme" argument="--renz_2" help="provide the second restriction enzyme used" >
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63 <expand macro="enzymes"/>
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64 </param>
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65 </when>
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66 </conditional>
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67
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68 <section name="options_advanced" title="advanced options" expanded="False">
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69 <expand macro="common_advanced"/>
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70 <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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71 <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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72 <expand macro="rescue_barcode"/>
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73 <expand macro="process_adapter"/>
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74 </section>
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75
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76 <expand macro="process_filter"/>
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77 <expand macro="process_output_types"/>
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78 <expand macro="in_log"/>
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79 </inputs>
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80
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81 <outputs>
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82 <expand macro="out_log"/>
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83 <expand macro="process_outputs"/>
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84 </outputs>
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85 <tests>
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86 <!-- single single ended input, no filtering (hence no capturing) + log -->
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87 <test>
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88 <param name="input_type|input_type_select" value="single"/>
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89 <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
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90 <param name="input_type|barcode_encoding" value="--inline_null"/>
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91 <param name="barcode" value="procrad/barcodes"/>
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92 <param name="options_enzyme|options_enzyme_selector" value="1"/>
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93 <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
94 <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
95 <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
96 <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
97 <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
98 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
99 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
100 <!-- 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
101 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
102 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
103 <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
104 <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
105 <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
106 <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
107 <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
108 <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:
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109 <param name="filter_cond|filter_select" value="yes"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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110 <param name="filter_cond|discard" value="true"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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111 <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:
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112 <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
113 <param name="filter_cond|remove" value="-c" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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114 <param name="filter_cond|filter_illumina" value="--filter_illumina" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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115 <param name="capture" value="true"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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116 <param name="outype" value="gzfastq"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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117 <assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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118 <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
119 <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:
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120 <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
121 <has_text text="-c" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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122 <has_text text="--filter_illumina" />
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
123 </assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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124 <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
125 <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
126 </output_collection>
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="discarded" count="2">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
128 <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
129 <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
130 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
131 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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132 <!-- 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
133 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
134 <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
135 <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
136 <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
137 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
138 <collection type="paired">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
139 <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
140 <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
141 </collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
142 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
143 </collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
144 </param>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
145 <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
146 <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
147 <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
148 <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
149 <param name="filter_cond|len_limit" value="50"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
150 <param name="capture" value="true"/>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
151 <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
152 <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
153 <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
154 <assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
155 <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
156 </assert_command>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
157 <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
158 <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
159 <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
160 <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
161 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
162 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
163 <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
164 <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
165 <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
166 <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
167 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
168 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
169 <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
170 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
171 <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
172 <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
173 </element>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
174 </output_collection>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
175 </test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
176 <!-- 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
177 <test>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
178 <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
179 <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
180 <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
181 <element name="reads">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
diff changeset
182 <collection type="paired">
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
iuc
parents:
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183 <element name="forward" value="procrad/R1.fq.gzip" ftype="fastqsanger.gz" />
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184 <element name="reverse" value="procrad/R2.fq.gzip" ftype="fastqsanger.gz"/>
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185 </collection>
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186 </element>
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187 </collection>
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188 </param>
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189 <param name="barcode" value="procrad/barcodes"/>
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190 <param name="options_enzyme|options_enzyme_selector" value="2"/>
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191 <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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192 <param name="options_enzyme|enzyme2" value="ecoRI"/>
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193 <param name="options_advanced|truncate" value="70" />
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194 <param name="options_advanced|rescue_cond|rescue" value="-r"/>
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195 <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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196 <param name="options_advanced|rescue_cond|barcode_dist_2" value="2" />
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197 <param name="options_advanced|bestrad" value="--bestrad" />
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198 <param name="options_advanced|retain_header" value="true"/>
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199 <param name="options_advanced|disable_rad_check" value="--disable_rad_check" />
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200 <param name="options_advanced|adapter_1" value="" />
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201 <param name="options_advanced|adapter_2" value="" />
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202 <param name="options_advanced|adapter_mm" value="" />
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203 <param name="outype" value="fasta"/>
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204 <assert_command>
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205 <has_text text="-e ecoRI" />
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206 <has_text text="--renz_2 ecoRI" />
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207 <has_text text="-t 70" />
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208 <has_text text="-r" />
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209 <has_text text="--bestrad" />
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210 <has_text text="--retain_header" />
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211 <has_text text="--disable_rad_check" />
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212 <has_text text="--barcode_dist_1 2" />
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213 <has_text text="--barcode_dist_2 2" />
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214 <has_text text="--adapter_mm 2" />
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215 </assert_command>
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216 <output_collection name="demultiplexed_paired" type="list:paired" count="40">
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217 <element name="PopA_01">
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218 <element name="forward" file="demultiplexed/PopA_01.1.fa" ftype="fasta"/>
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219 <element name="reverse" file="demultiplexed/PopA_01.2.fa" ftype="fasta"/>
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220 </element>
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221 </output_collection>
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222 <output_collection name="remaining" type="list:paired" count="40">
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223 <element name="PopA_01">
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224 <element name="forward" file="demultiplexed/PopA_01.rem.1.fa" ftype="fasta" />
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225 <element name="reverse" file="demultiplexed/PopA_01.rem.2.fa" ftype="fasta" />
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226 </element>
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227 </output_collection>
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228 </test>
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229 </tests>
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230
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231 <help>
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232 <![CDATA[
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233 .. class:: infomark
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234
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235 **What it does**
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236
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237 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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238
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239 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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240
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241 - handle data that is barcoded, either inline or using an index, or unbarcoded.
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242 - use combinatorial barcodes.
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243 - check and correct for a restriction enzyme cutsite for single or double-digested data.
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244 - filter adapter sequence while allowing for sequencing error in the adapter pattern.
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245 - process individual files or whole directories of files.
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246 - directly read gzipped data
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247 - filter reads based on Illumina's Chastity filter
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248
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249 **Help**
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250
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251 Input files:
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252
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253 - A set of one or more FASTQ files (either selected manually, a dataset list, or a paired dataset list)
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254
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255 - Barcode File
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256
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257 The barcode file is a very simple format:
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258
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259 ======= ===========
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260 Barcode Sample name
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261 ======= ===========
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262 ATGGGG PopA_01
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263 GGGTAA PopA_02
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264 AGGAAA PopA_03
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265 TTTAAG PopA_04
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266 GGTGTG PopA_05
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267 TGATGT PopA_06
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268 ======= ===========
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269
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270 Combinatorial barcodes are specified, one per column, separated by a tab:
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271
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272 ======== ======== ===========
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273 Barcode1 Barcode2 Sample name
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274 ======== ======== ===========
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275 CGATA ACGTA PopA_01
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276 CGGCG CGTA PopA_02
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277 GAAGC CGTA PopA_03
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278 GAGAT CGTA PopA_04
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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279 CGATA AGCA PopA_05
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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280 CGGCG AGCA PopA_06
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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281 ======== ======== ===========
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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282
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283 The sample name column can be omitted. Then the Barcodes are used for naming the output files.
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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284
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285 @STACKS_INFOS@
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286 ]]>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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287 </help>
3d413e8cb277 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460
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288 <expand macro="citation" />
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289 </tool>