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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/falco commit a71120623d1dc818a107ca32f2c232fd47d819ea
author iuc
date Fri, 27 Sep 2024 17:41:19 +0000
parents 0f4aadf6988c
children
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1:0f4aadf6988c 2:2b29a20e9869
1 <tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 1 <tool id="falco" name="Falco" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description> 2 <description>An alternative, more performant implementation of FastQC for high throughput sequence quality control</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.2.3</token> 4 <token name="@TOOL_VERSION@">1.2.4</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">falco</xref> 8 <xref type="bio.tools">falco</xref>
9 </xrefs> 9 </xrefs>
72 <data format="txt" name="summary_file" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: SummaryData"> 72 <data format="txt" name="summary_file" from_work_dir="summary.txt" label="${tool.name} on ${on_string}: SummaryData">
73 <filter>generate_summary</filter> 73 <filter>generate_summary</filter>
74 </data> 74 </data>
75 </outputs> 75 </outputs>
76 <tests> 76 <tests>
77 <test expect_num_outputs="2"> 77 <!-- Test with fastq input -->
78 <param name="input_file" value="1000trimmed.fastq"/> 78 <test expect_num_outputs="2">
79 <output name="html_file" file="fastqc_report.html" ftype="html" lines_diff="2"/> 79 <param name="input_file" value="1000trimmed.fastq"/>
80 <output name="text_file" file="fastqc_data.txt" ftype="txt"/> 80 <output name="html_file" ftype="html">
81 <assert_contents>
82 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
83 </assert_contents>
84 </output>
85 <!-- two lines diff to allow for reported version to change -->
86 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
87 </test>
88 <!-- Test with fastq.gz input -->
89 <test expect_num_outputs="2">
90 <param name="input_file" value="1000trimmed.fastq.gz"/>
91 <output name="html_file" ftype="html">
92 <assert_contents>
93 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq_gz - report.+"/>
94 </assert_contents>
95 </output>
96 <!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
97 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="4"/>
98 </test>
99 <!-- Test with BAM input -->
100 <test expect_num_outputs="2">
101 <param name="input_file" value="hisat_output_1.bam"/>
102 <output name="html_file" ftype="html">
103 <assert_contents>
104 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; hisat_output_1_bam - report.+"/>
105 </assert_contents>
106 </output>
107 <!-- four lines diff to allow for reported version to change; two more to accomodate changed input file name -->
108 <output name="text_file" file="fastqc_data_hisat.txt" ftype="txt" lines_diff="4"/>
109 </test>
110 <!-- Test summary file option -->
111 <test expect_num_outputs="3">
112 <param name="input_file" value="1000trimmed.fastq"/>
113 <param name="generate_summary" value="true"/>
114 <output name="html_file" ftype="html">
115 <assert_contents>
116 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
117 </assert_contents>
118 </output>
119 <output name="text_file" file="fastqc_data.txt" ftype="txt" lines_diff="2"/>
120 <output name="summary_file" file="fastqc_data_summary.txt" ftype="txt"/>
81 </test> 121 </test>
82 <test expect_num_outputs="2"> 122 <test expect_num_outputs="2">
83 <param name="input_file" value="1000trimmed.fastq"/> 123 <param name="input_file" value="1000trimmed.fastq"/>
84 <param name="contaminants" value="contaminant_list.txt" ftype="tabular"/> 124 <param name="contaminants" value="contaminant_list.txt" ftype="tabular"/>
85 <output name="html_file" file="fastqc_report_contaminants.html" ftype="html" lines_diff="2"/> 125 <output name="html_file" ftype="html">
86 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt"/> 126 <assert_contents>
127 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
128 </assert_contents>
129 </output>
130 <output name="text_file" file="fastqc_data_contaminants.txt" ftype="txt" lines_diff="2"/>
87 </test> 131 </test>
88 <test expect_num_outputs="2"> 132 <test expect_num_outputs="2">
89 <param name="input_file" value="1000trimmed.fastq"/> 133 <param name="input_file" value="1000trimmed.fastq"/>
90 <param name="adapters" value="adapter_list.txt" ftype="tabular"/> 134 <param name="adapters" value="adapter_list.txt" ftype="tabular"/>
91 <output name="html_file" file="fastqc_report_adapters.html" ftype="html" lines_diff="2"/> 135 <output name="html_file" ftype="html">
92 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt"/> 136 <assert_contents>
93 </test> 137 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
94 <test expect_num_outputs="2"> 138 </assert_contents>
139 </output>
140 <output name="text_file" file="fastqc_data_adapters.txt" ftype="txt" lines_diff="2"/>
141 </test>
142 <test expect_num_outputs="3">
95 <param name="input_file" value="1000trimmed.fastq"/> 143 <param name="input_file" value="1000trimmed.fastq"/>
96 <param name="limits" value="limits.txt" ftype="txt"/> 144 <param name="limits" value="limits.txt" ftype="txt"/>
97 <output name="html_file" file="fastqc_report_customlimits.html" ftype="html" lines_diff="2"/> 145 <param name="generate_summary" value="true"/>
98 <output name="text_file" file="fastqc_data_customlimits.txt" ftype="txt"/> 146 <output name="html_file" ftype="html">
147 <assert_contents>
148 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
149 </assert_contents>
150 </output>
151 <output name="summary_file" file="fastqc_data_customlimits_summary.txt" ftype="txt"/>
99 </test> 152 </test>
100 <!-- ## The kmers param is ignored in Falco and always set to 7. If this ever gets reconsidered, this test could be uncommented. 153 <!-- ## The kmers param is ignored in Falco and always set to 7. If this ever gets reconsidered, this test could be uncommented.
101 <test expect_num_outputs="2"> 154 <test expect_num_outputs="2">
102 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/> 155 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
103 <param name="kmers" value="7"/> 156 <param name="kmers" value="7"/>
114 <param name="input_file" value="1000trimmed.fastq"/> 167 <param name="input_file" value="1000trimmed.fastq"/>
115 <param name="min_length" value="108"/> 168 <param name="min_length" value="108"/>
116 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/> 169 <output name="html_file" file="fastqc_report_min_length.html" ftype="html" lines_diff="2"/>
117 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/> 170 <output name="text_file" file="fastqc_data_min_length.txt" ftype="txt"/>
118 </test> --> 171 </test> -->
119 <test expect_num_outputs="3"> 172 <test expect_num_outputs="2">
120 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/> 173 <param name="input_file" value="1000trimmed.fastq" ftype="fastq"/>
121 <param name="nogroup" value="--nogroup"/> 174 <param name="nogroup" value="--nogroup"/>
122 <param name="generate_summary" value="true"/> 175 <output name="html_file" ftype="html">
123 <output name="html_file" file="fastqc_report_nogroup.html" ftype="html" lines_diff="2"/> 176 <assert_contents>
124 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt"/> 177 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
125 <output name="summary_file" file="fastqc_data_nogroup_summary.txt" ftype="txt"/> 178 </assert_contents>
126 <assert_command> 179 </output>
127 <has_text text="--nogroup"/> 180 <output name="text_file" file="fastqc_data_nogroup.txt" ftype="txt" lines_diff="2"/>
128 </assert_command>
129 </test> 181 </test>
130 <test expect_num_outputs="3"> 182 <test expect_num_outputs="3">
131 <param name="input_file" value="1000trimmed.fastq"/> 183 <param name="input_file" value="1000trimmed.fastq"/>
132 <param name="subsample" value="10"/> 184 <param name="subsample" value="10"/>
133 <param name="generate_summary" value="true"/> 185 <param name="generate_summary" value="true"/>
134 <output name="html_file" file="fastqc_report_subsample.html" ftype="html" lines_diff="2"/> 186 <output name="html_file" ftype="html">
135 <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt"/> 187 <assert_contents>
188 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
189 </assert_contents>
190 </output>
191 <output name="text_file" file="fastqc_report_subsample.txt" ftype="txt" lines_diff="2"/>
136 <output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/> 192 <output name="summary_file" file="fastqc_report_subsample_summary.txt" ftype="txt"/>
137 </test> 193 </test>
138 <test expect_num_outputs="3"> 194 <test expect_num_outputs="3">
139 <param name="input_file" value="1000trimmed.fastq"/> 195 <param name="input_file" value="1000trimmed.fastq"/>
140 <param name="bisulfite" value="-bisulfite"/> 196 <param name="bisulfite" value="-bisulfite"/>
141 <param name="generate_summary" value="true"/> 197 <param name="generate_summary" value="true"/>
142 <output name="html_file" file="fastqc_report_bisulfite.html" ftype="html" lines_diff="2"/> 198 <output name="html_file" ftype="html">
143 <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt"/> 199 <assert_contents>
200 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
201 </assert_contents>
202 </output>
203 <output name="text_file" file="fastqc_report_bisulfite.txt" ftype="txt" lines_diff="2"/>
144 <output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/> 204 <output name="summary_file" file="fastqc_report_bisulfite_summary.txt" ftype="txt"/>
145 </test> 205 </test>
146 <test expect_num_outputs="3"> 206 <test expect_num_outputs="2">
147 <param name="input_file" value="1000trimmed.fastq"/> 207 <param name="input_file" value="1000trimmed.fastq"/>
148 <param name="reverse_complement" value="-reverse-complement"/> 208 <param name="reverse_complement" value="-reverse-complement"/>
149 <param name="generate_summary" value="true"/> 209 <output name="html_file" ftype="html">
150 <output name="html_file" file="fastqc_report_reverse_complement.html" ftype="html" lines_diff="2"/> 210 <assert_contents>
151 <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt"/> 211 <has_line_matching expression="&lt;html&gt;&lt;head&gt;.+&lt;title&gt; 1000trimmed_fastq - report.+"/>
152 <output name="summary_file" file="fastqc_report_reverse_complement_summary.txt" ftype="txt"/> 212 </assert_contents>
213 </output>
214 <output name="text_file" file="fastqc_report_reverse_complement.txt" ftype="txt" lines_diff="2"/>
153 </test> 215 </test>
154 </tests> 216 </tests>
155 <help><![CDATA[ 217 <help><![CDATA[
156 **What it does** 218 **What it does**
157 219
158 Falco_ is a high-speed emulation of the popular FastQC software for quality control of sequencing data. 220 Falco_ is a high-speed emulation of the popular FastQC software for quality control of sequencing data.
159 221
160 💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC. 222 💚️ With its superior performance Falco saves computational resources and gives you back results faster than FastQC.
161 223
162 We recommend it for most use cases (but see below for exceptions). 💚️ 224 We recommend it for most use cases (but see below for rare exceptions). 💚️
163 225
164 The main functions of Falco are very similar to those of FastQC: 226 The main functions of Falco are very similar to those of FastQC:
165 227
166 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant), 228 - Import of data from BAM, SAM or FastQ/FastQ.gz files (any variant),
167 - Providing a quick overview to tell you in which areas there may be problems 229 - Providing a quick overview to tell you in which areas there may be problems
168 - Summary graphs and tables to quickly assess your data 230 - Summary graphs and tables to quickly assess your data
169 - Export of results to an HTML based permanent report 231 - Export of results to an HTML-based report
170 - Offline operation to allow automated generation of reports without running the interactive application 232
171 233
172 .. class:: infomark 234 .. class:: infomark
173 235
174 The plain text report generated by Falco can be used as a "FastQC" report in MultiQC and its data is very similar though not 100% identical to that generated by FastQC on the same inputs. 236 The plain text report generated by Falco can be used as a "FastQC" report in MultiQC and its data is very similar though not 100% identical to that generated by FastQC on the same inputs.
175 237
179 241
180 - your input is bz2-compressed fastq 242 - your input is bz2-compressed fastq
181 243
182 Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC. 244 Falco doesn't currently support fastq.bz2 as input format meaning Galaxy has to perform a relatively slow format conversion before running the tool, which together makes the analysis slower than with FastQC.
183 245
184 - you are interested in PolyA and PolyG statistics in the Adapter Content section of the quality report 246 - you need the HTML report to be viewable offline
185 247
186 Falco doesn't currently calculate statistics for these "Adapters" by default. 248 The current version of Falco relies on plotly to generate the graphs in the HTML report dynamically each time it's viewed.
187 249 MultiQC plots generated from Falco's raw data output are, of course, viewable offline just like the ones generated from FastQC output.
188 - your input consists of *mapped* reads in SAM/BAM format
189
190 Due to a bug in the current version of Falco, reads mapped to the reverse strand of the reference genome are not handled correctly and reported metrics are wrong!
191 250
192 ----- 251 -----
193 252
194 **Inputs and outputs** 253 **Inputs and outputs**
195 254