Mercurial > repos > iuc > stacks2_clonefilter
comparison stacks_clonefilter.xml @ 3:289b7d6b69a4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"
author | iuc |
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date | Tue, 27 Apr 2021 09:27:26 +0000 |
parents | 2f1d464ebfd2 |
children | 42201b90e3f4 |
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2:2f1d464ebfd2 | 3:289b7d6b69a4 |
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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 |