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comparison stacks_clonefilter.xml @ 2:2f1d464ebfd2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
author iuc
date Thu, 16 Jul 2020 07:30:45 -0400
parents b75174403a65
children 289b7d6b69a4
comparison
equal deleted inserted replaced
1:b75174403a65 2:2f1d464ebfd2
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_cmd"/> 7 <expand macro="version_cmd"/>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 @FASTQ_INPUT_FUNCTIONS@ 9 @FASTQ_INPUT_FUNCTIONS@
10 10
11 trap ">&2 cat '$output_log'" err exit &&
11 mkdir stacks_inputs stacks_outputs && 12 mkdir stacks_inputs stacks_outputs &&
12 13
13 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select) 14 #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
14 $link_command 15 $link_command
15 16
35 $retain_oligo 36 $retain_oligo
36 ## only supports fastq.gz output since the 37 ## only supports fastq.gz output since the
37 ## the program outputs empty files for fasta/fastq 38 ## the program outputs empty files for fasta/fastq
38 -y gzfastq 39 -y gzfastq
39 @TEE_APPEND_LOG@ 40 @TEE_APPEND_LOG@
40 @CAT_LOG_TO_STDERR@
41 41
42 ## move outputs such that Galaxy can find them 42 ## move outputs such that Galaxy can find them
43 #if $capture: 43 #if $capture:
44 #if $input_type.input_type_select == "single" 44 #if $input_type.input_type_select == "single"
45 && mv stacks_outputs/*.discards.fq.gz '$discarded' 45 && mv stacks_outputs/*.discards.fq.gz '$discarded'
55 && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse' 55 && mv stacks_outputs/*.2.fq.gz '$clean_pair.reverse'
56 #end if 56 #end if
57 ]]></command> 57 ]]></command>
58 <inputs> 58 <inputs>
59 <expand macro="fastq_input_bc"/> 59 <expand macro="fastq_input_bc"/>
60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> 60 <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
61 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/> 61 <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/>
62 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/> 62 <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/>
63 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" /> 63 <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)"/>
64 <expand macro="in_log"/> 64 <expand macro="in_log"/>
65 </inputs> 65 </inputs>
66 <outputs> 66 <outputs>
67 <expand macro="out_log"/> 67 <expand macro="out_log"/>
68 <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> 68 <expand macro="fastq_output_filter"/>
69 <filter>input_type['input_type_select'] == 'single'</filter>
70 </data>
71 <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
72 <filter>input_type['input_type_select'] == 'paired'</filter>
73 </collection>
74 <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
75 <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
76 </data>
77 <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
78 <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
79 </collection>
80 </outputs> 69 </outputs>
81 <tests> 70 <tests>
82 <!-- single end, defaults--> 71 <!-- single end, defaults-->
83 <test> 72 <test expect_num_outputs="2">
84 <conditional name="input_type"> 73 <conditional name="input_type">
85 <param name="input_type_select" value="single" /> 74 <param name="input_type_select" value="single"/>
86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 75 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
87 </conditional> 76 </conditional>
88 <param name="oligo_len_1" value="6" /> 77 <param name="oligo_len_1" value="6"/>
89 <param name="add_log" value="yes" /> 78 <param name="add_log" value="yes"/>
90 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/> 79 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
91 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 80 <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
92 </test> 81 </test>
93 <!-- single end, alt BCencoding, capture--> 82 <!-- single end, alt BCencoding, capture-->
94 <test> 83 <test expect_num_outputs="3">
95 <conditional name="input_type"> 84 <conditional name="input_type">
96 <param name="input_type_select" value="single" /> 85 <param name="input_type_select" value="single"/>
97 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> 86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
98 <param name="barcode_encoding" value="--index_null" /> 87 <param name="barcode_encoding" value="--index_null"/>
99 </conditional> 88 </conditional>
100 <param name="capture" value="-D" /> 89 <param name="capture" value="-D"/>
101 <param name="oligo_len_1" value="6" /> 90 <param name="oligo_len_1" value="6"/>
102 <assert_command> 91 <assert_command>
103 <has_text text="-D" /> 92 <has_text text="-D"/>
104 </assert_command> 93 </assert_command>
105 <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 94 <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
106 <output name="discarded" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 95 <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/>
96 <output name="discarded" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
107 </test> 97 </test>
108 <!-- paired end, defaults--> 98 <!-- paired end, defaults-->
109 <test> 99 <test expect_num_outputs="4">
110 <conditional name="input_type"> 100 <conditional name="input_type">
111 <param name="input_type_select" value="paired" /> 101 <param name="input_type_select" value="paired"/>
112 <param name="fqinputs"> 102 <param name="fqinputs">
113 <collection type="paired"> 103 <collection type="paired">
114 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> 104 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
115 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> 105 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
116 </collection> 106 </collection>
117 </param> 107 </param>
118 </conditional> 108 </conditional>
119 <param name="oligo_len_1" value="6" /> 109 <param name="oligo_len_1" value="6"/>
110 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
120 <output_collection name="clean_pair" type="paired"> 111 <output_collection name="clean_pair" type="paired">
121 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> 112 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
122 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> 113 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
123 </output_collection> 114 </output_collection>
124 </test> 115 </test>
125 <!-- paired end, non defaults --> 116 <!-- paired end, non defaults -->
126 <test> 117 <test expect_num_outputs="7">
127 <conditional name="input_type"> 118 <conditional name="input_type">
128 <param name="input_type_select" value="paired" /> 119 <param name="input_type_select" value="paired"/>
129 <param name="fqinputs"> 120 <param name="fqinputs">
130 <collection type="paired"> 121 <collection type="paired">
131 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" /> 122 <element name="forward" value="clonefilter/R1_0001.1.fq.gz" ftype="fastqsanger.gz"/>
132 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" /> 123 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
133 </collection> 124 </collection>
134 </param> 125 </param>
135 </conditional> 126 </conditional>
136 <param name="oligo_len_1" value="6" /> 127 <param name="oligo_len_1" value="6"/>
137 <param name="capture" value="-D" /> 128 <param name="capture" value="-D"/>
138 <param name="retain_oligo" value="--retain_oligo" /> 129 <param name="retain_oligo" value="--retain_oligo"/>
139 <assert_command> 130 <assert_command>
140 <has_text text="--retain_oligo" /> 131 <has_text text="--retain_oligo"/>
141 </assert_command> 132 </assert_command>
133 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
142 <output_collection name="clean_pair" type="paired"> 134 <output_collection name="clean_pair" type="paired">
143 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> 135 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
144 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> 136 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
145 </output_collection> 137 </output_collection>
146 <output_collection name="discarded_pair" type="paired"> 138 <output_collection name="discarded_pair" type="paired">
147 <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" /> 139 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
148 <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" /> 140 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
149 </output_collection> 141 </output_collection>
150 </test> 142 </test>
151 </tests> 143 </tests>
152 <help> 144 <help>
153 <![CDATA[ 145 <![CDATA[
156 The clone_filter program is designed to identify PCR clones. 148 The clone_filter program is designed to identify PCR clones.
157 149
158 @STACKS_INFOS@ 150 @STACKS_INFOS@
159 ]]> 151 ]]>
160 </help> 152 </help>
161 <expand macro="citation" /> 153 <expand macro="citation"/>
162 </tool> 154 </tool>