Mercurial > repos > iuc > stacks2_clonefilter

comparison stacks_clonefilter.xml @ 3:289b7d6b69a4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author iuc
date Tue, 27 Apr 2021 09:27:26 +0000
parents 2f1d464ebfd2
children 42201b90e3f4
comparison
equal deleted inserted replaced
2:2f1d464ebfd2 3:289b7d6b69a4
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 <expand macro="fastq_output_filter"/> 68 <expand macro="fastq_output_filter" format="fastqsanger.gz"/>
69 </outputs> 69 </outputs>
70 <tests> 70 <tests>
71 <!-- single end, defaults--> 71 <!-- single end, defaults-->
72 <test expect_num_outputs="2"> 72 <test expect_num_outputs="2">
73 <conditional name="input_type"> 73 <conditional name="input_type">
74 <param name="input_type_select" value="single"/> 74 <param name="input_type_select" value="single"/>
75 <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"/>
76 </conditional> 76 </conditional>
77 <param name="oligo_len_1" value="6"/> 77 <param name="oligo_len_1" value="6"/>
78 <param name="add_log" value="yes"/> 78 <param name="add_log" value="yes"/>
79 <assert_command>
80 <has_text text="--oligo_len_1 6"/>
81 <not_has_text text="-D"/>
82 </assert_command>
79 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/> 83 <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/>
80 <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> 84 <output name="clean" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
81 </test> 85 </test>
82 <!-- single end, alt BCencoding, capture--> 86 <!-- single end, alt BCencoding, capture-->
83 <test expect_num_outputs="3"> 87 <test expect_num_outputs="3">
84 <conditional name="input_type"> 88 <conditional name="input_type">
85 <param name="input_type_select" value="single"/> 89 <param name="input_type_select" value="single"/>
86 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/> 90 <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>
87 <param name="barcode_encoding" value="--index_null"/> 91 <param name="barcode_encoding" value="--index_null"/>
88 </conditional> 92 </conditional>
89 <param name="capture" value="-D"/> 93 <param name="capture" value="true"/>
90 <param name="oligo_len_1" value="6"/> 94 <param name="oligo_len_1" value="6"/>
91 <assert_command> 95 <assert_command>
96 <has_text text="--oligo_len_1 6"/>
92 <has_text text="-D"/> 97 <has_text text="-D"/>
93 </assert_command> 98 </assert_command>
94 <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output> 99 <output name="output_log" ftype="txt"><assert_contents><has_text text="5 pairs of reads input."/></assert_contents></output>
95 <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.single-alt.gz"/> 100 <output name="clean" compare="diff" 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"/> 101 <output name="discarded" compare="diff" ftype="fastqsanger.gz" file="clonefilter/Discarded1_0001.1.1.fq.single.gz"/>
97 </test> 102 </test>
98 <!-- paired end, defaults--> 103 <!-- paired end, defaults-->
99 <test expect_num_outputs="4"> 104 <test expect_num_outputs="4">
100 <conditional name="input_type"> 105 <conditional name="input_type">
101 <param name="input_type_select" value="paired"/> 106 <param name="input_type_select" value="paired"/>
105 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/> 110 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
106 </collection> 111 </collection>
107 </param> 112 </param>
108 </conditional> 113 </conditional>
109 <param name="oligo_len_1" value="6"/> 114 <param name="oligo_len_1" value="6"/>
115 <assert_command>
116 <has_text text="--oligo_len_1 6"/>
117 <not_has_text text="--oligo_len_2"/>
118 <not_has_text text="-D"/>
119 </assert_command>
110 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output> 120 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
111 <output_collection name="clean_pair" type="paired"> 121 <output_collection name="clean_pair" type="paired" count="2"/>
112 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
113 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
114 </output_collection>
115 </test> 122 </test>
116 <!-- paired end, non defaults --> 123 <!-- paired end, non defaults -->
117 <test expect_num_outputs="7"> 124 <test expect_num_outputs="7">
118 <conditional name="input_type"> 125 <conditional name="input_type">
119 <param name="input_type_select" value="paired"/> 126 <param name="input_type_select" value="paired"/>
123 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/> 130 <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" ftype="fastqsanger.gz"/>
124 </collection> 131 </collection>
125 </param> 132 </param>
126 </conditional> 133 </conditional>
127 <param name="oligo_len_1" value="6"/> 134 <param name="oligo_len_1" value="6"/>
128 <param name="capture" value="-D"/> 135 <param name="oligo_len_2" value="6"/>
129 <param name="retain_oligo" value="--retain_oligo"/> 136 <param name="capture" value="true"/>
137 <param name="retain_oligo" value="true"/>
130 <assert_command> 138 <assert_command>
139 <has_text text="--oligo_len_1 6"/>
140 <has_text text="--oligo_len_2 6"/>
141 <has_text text="-D"/>
131 <has_text text="--retain_oligo"/> 142 <has_text text="--retain_oligo"/>
132 </assert_command> 143 </assert_command>
133 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output> 144 <output name="output_log" ftype="txt"><assert_contents><has_text text="4 pairs of reads input."/></assert_contents></output>
134 <output_collection name="clean_pair" type="paired"> 145 <output_collection name="clean_pair" type="paired" count="2"/>
135 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/> 146 <output_collection name="discarded_pair" type="paired" count="2"/>
136 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
137 </output_collection>
138 <output_collection name="discarded_pair" type="paired">
139 <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed1_0001.1.1.fq.gz"/>
140 <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="clonefilter/Removed2_0001.2.2.fq.gz"/>
141 </output_collection>
142 </test> 147 </test>
143 </tests> 148 </tests>
144 <help> 149 <help>
145 <![CDATA[ 150 <![CDATA[
146 .. class:: infomark 151 .. class:: infomark