Mercurial > repos > matthias > stacks2_clonefilter
comparison stacks_clonefilter.xml @ 3:4758a347d62e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
| author | matthias |
|---|---|
| date | Tue, 18 Dec 2018 13:06:09 -0500 |
| parents | 223e7778451a |
| children | c4ed7dacee9b |
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| 2:223e7778451a | 3:4758a347d62e |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_cmd"/> | 8 <expand macro="version_cmd"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 | |
| 11 #if $data_type.dt_select == "single" | 10 #if $data_type.dt_select == "single" |
| 12 | 11 |
| 13 #if $data_type.fname.is_of_type('fastqsanger') | 12 #if $data_type.fname.is_of_type('fastqsanger') |
| 14 #set $ext = ".fq" | 13 #set $ext = ".fq" |
| 15 #set inputype = "fastq" | 14 #set inputype = "fastq" |
| 32 ln -s '$data_type.fwd' R1$ext && | 31 ln -s '$data_type.fwd' R1$ext && |
| 33 ln -s '$data_type.rev' R2$ext && | 32 ln -s '$data_type.rev' R2$ext && |
| 34 #end if | 33 #end if |
| 35 | 34 |
| 36 | 35 |
| 37 mkdir clone_outputs | 36 mkdir outputs |
| 38 | 37 |
| 39 && | 38 && |
| 40 | 39 |
| 41 clone_filter | 40 clone_filter |
| 42 #if $data_type.dt_select == 'single': | 41 #if $data_type.dt_select == 'single': |
| 46 -2 R2$ext | 45 -2 R2$ext |
| 47 #end if | 46 #end if |
| 48 | 47 |
| 49 -i $inputype | 48 -i $inputype |
| 50 | 49 |
| 51 -o clone_outputs | 50 -o outputs |
| 52 $capture | 51 $capture |
| 53 | 52 $data_type.barcode_encoding |
| 54 #if $oligo_len_1 | 53 #if $oligo_len_1 |
| 55 --oligo_len_1 $oligo_len_1 | 54 --oligo_len_1 $oligo_len_1 |
| 56 $data_type.barcode_encoding | |
| 57 #end if | 55 #end if |
| 58 #if $oligo_len_2 | 56 #if $oligo_len_2 |
| 59 --oligo_len_2 $oligo_len_2 | 57 --oligo_len_2 $oligo_len_2 |
| 60 #end if | 58 #end if |
| 61 $retain_oligo | 59 $retain_oligo |
| 62 ## only supports fastq.gz output since the | 60 ## only supports fastq.gz output since the |
| 63 ## the program outputs empty files for fasta/fastq | 61 ## the program outputs empty files for fasta/fastq |
| 64 -y gzfastq | 62 -y gzfastq |
| 65 | |
| 66 ]]></command> | 63 ]]></command> |
| 67 <inputs> | 64 <inputs> |
| 68 <conditional name="data_type"> | 65 <conditional name="data_type"> |
| 69 <param name="dt_select" type="select" label="Single or Paired-end"> | 66 <param name="dt_select" type="select" label="Single or Paired-end"> |
| 70 <option value="single">Single</option> | 67 <option value="single">Single</option> |
| 71 <option value="pair">Pair</option> | 68 <option value="pair">Pair</option> |
| 72 </param> | 69 </param> |
| 73 <when value="single"> | 70 <when value="single"> |
| 74 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> | 71 <param name="fname" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ" /> |
| 75 <param name="barcode_encoding" type="select" label="Barcode location"> | 72 <param name="barcode_encoding" type="select" label="Barcode location"> |
| 76 <expand macro="barcode_encoding_single" /> | 73 <expand macro="barcode_encoding_single" type="Random oligo"/> |
| 77 </param> | 74 </param> |
| 78 | 75 |
| 79 </when> | 76 </when> |
| 80 <when value="pair"> | 77 <when value="pair"> |
| 81 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> | 78 <param name="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward FASTQ" /> |
| 82 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> | 79 <param name="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse FASTQ" /> |
| 83 <param name="barcode_encoding" type="select" label="Barcode location"> | 80 <param name="barcode_encoding" type="select" label="Barcode location"> |
| 84 <expand macro="barcode_encoding_pair" /> | 81 <expand macro="barcode_encoding_pair" type="Random oligo"/> |
| 85 </param> | 82 </param> |
| 86 </when> | 83 </when> |
| 87 </conditional> | 84 </conditional> |
| 88 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> | 85 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> |
| 89 <param name="oligo_len_1" optional="true" type="integer" label="length of the single-end oligo sequence in data set"/> | 86 <param name="oligo_len_1" type="integer" value="0" label="length of the single-end oligo sequence in data set"/> |
| 90 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> | 87 <param name="oligo_len_2" optional="true" type="integer" label="length of the paired-end oligo sequence in data set"/> |
| 91 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" /> | 88 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="do not trim off the random oligo sequence (if oligo is inline)" /> |
| 92 | 89 |
| 93 </inputs> | 90 </inputs> |
| 94 <outputs> | 91 <outputs> |
| 95 <data format="fastqsanger.gz" name="clean" from_work_dir="clone_outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> | 92 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> |
| 96 <filter>data_type['dt_select'] == 'single'</filter> | 93 <filter>data_type['dt_select'] == 'single'</filter> |
| 97 </data> | 94 </data> |
| 98 | 95 |
| 99 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="clone_outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads"> | 96 <data format="fastqsanger.gz" name="clean_fwd" from_work_dir="outputs/R1.1.fq.gz" label="${tool.name} on ${on_string} Forward reads"> |
| 100 <filter>data_type['dt_select'] == 'pair'</filter> | 97 <filter>data_type['dt_select'] == 'pair'</filter> |
| 101 </data> | 98 </data> |
| 102 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="clone_outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads"> | 99 <data format="fastqsanger.gz" name="clean_rev" from_work_dir="outputs/R2.2.fq.gz" label="${tool.name} on ${on_string} Reverse reads"> |
| 103 <filter>data_type['dt_select'] == 'pair'</filter> | 100 <filter>data_type['dt_select'] == 'pair'</filter> |
| 104 </data> | 101 </data> |
| 105 </outputs> | 102 </outputs> |
| 106 <tests> | 103 <tests> |
| 104 <!-- single end, defaults--> | |
| 107 <test> | 105 <test> |
| 108 <conditional name="data_type"> | 106 <conditional name="data_type"> |
| 109 <param name="dt_select" value="single" /> | 107 <param name="dt_select" value="single" /> |
| 110 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | 108 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> |
| 111 </conditional> | 109 </conditional> |
| 112 <param name="oligo_len_1" value="6" /> | 110 <param name="oligo_len_1" value="6" /> |
| 113 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> | 111 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> |
| 114 </test> | 112 </test> |
| 113 <!-- single end, alt BCencoding, capture--> | |
| 115 <test> | 114 <test> |
| 116 <conditional name="data_type"> | 115 <conditional name="data_type"> |
| 117 <param name="dt_select" value="single" /> | 116 <param name="dt_select" value="single" /> |
| 118 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | 117 <param name="fname" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> |
| 119 <param name="barcode_encoding" value="--index_null" /> | 118 <param name="barcode_encoding" value="--index_null" /> |
| 120 </conditional> | 119 </conditional> |
| 120 <param name="capture" value="-D" /> | |
| 121 <param name="oligo_len_1" value="6" /> | |
| 122 <assert_command> | |
| 123 <has_text text="-D" /> | |
| 124 </assert_command> | |
| 121 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | 125 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> |
| 122 </test> | 126 </test> |
| 127 <!-- paired end, defaults--> | |
| 123 <test> | 128 <test> |
| 124 <conditional name="data_type"> | 129 <conditional name="data_type"> |
| 125 <param name="dt_select" value="pair" /> | 130 <param name="dt_select" value="pair" /> |
| 126 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> | 131 <param name="fwd" ftype="fastqsanger" value="clonefilter/R1_0001.1.fq.gz" /> |
| 127 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> | 132 <param name="rev" ftype="fastqsanger" value="clonefilter/R2_0001.2.fq.gz" /> |
| 128 </conditional> | 133 </conditional> |
| 134 <param name="oligo_len_1" value="6" /> | |
| 129 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | 135 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> |
| 130 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> | 136 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> |
| 131 </test> | 137 </test> |
| 138 <!-- paired end, non defaults--> | |
| 132 <test> | 139 <test> |
| 133 <conditional name="data_type"> | 140 <conditional name="data_type"> |
| 134 <param name="dt_select" value="pair" /> | 141 <param name="dt_select" value="pair" /> |
| 135 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> | 142 <param name="fwd" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> |
| 136 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> | 143 <param name="rev" ftype="fastqsanger.gz" value="clonefilter/R2_0001.2.fq.gz" /> |
| 137 </conditional> | 144 </conditional> |
| 145 <param name="oligo_len_1" value="6" /> | |
| 146 <param name="capture" value="-D" /> | |
| 147 <param name="retain_oligo" value="--retain_oligo" /> | |
| 148 <assert_command> | |
| 149 <has_text text="--retain_oligo" /> | |
| 150 </assert_command> | |
| 138 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> | 151 <output name="clean_fwd" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> |
| 139 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> | 152 <output name="clean_rev" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz"/> |
| 140 </test> | 153 </test> |
| 141 </tests> | 154 </tests> |
| 142 <help> | 155 <help> |
| 143 <![CDATA[ | 156 <![CDATA[ |
| 144 .. class:: infomark | 157 .. class:: infomark |
| 145 | 158 |
| 146 | |
| 147 The clone_filter program is designed to identify PCR clones. | 159 The clone_filter program is designed to identify PCR clones. |
| 148 | 160 |
| 149 @STACKS_INFOS@ | 161 @STACKS_INFOS@ |
| 150 ]]> | 162 ]]> |
| 151 </help> | 163 </help> |