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comparison kallisto_quant.xml @ 10:4f9c4e6566e5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
author iuc
date Mon, 05 Jun 2023 22:06:44 +0000
parents 2568a3b975cb
children
comparison
equal deleted inserted replaced
9:2568a3b975cb 10:4f9c4e6566e5
30 --fragment-length $single_paired.fragment_length 30 --fragment-length $single_paired.fragment_length
31 --sd $single_paired.sd 31 --sd $single_paired.sd
32 '$single_reads' 32 '$single_reads'
33 #else: 33 #else:
34 $single_paired.lib_type 34 $single_paired.lib_type
35 #if str($single_paired.collection.collection_selector) == 'datasets': 35 #if str($single_paired.single_paired_selector) == 'paired_single':
36 #set $forward_reads = $single_paired.collection.forward 36 #set $forward_reads = $single_paired.forward
37 #set $reverse_reads = $single_paired.collection.reverse 37 #set $reverse_reads = $single_paired.reverse
38 #else: 38 #else:
39 #set $forward_reads = $single_paired.collection.reads.forward 39 #set $forward_reads = $single_paired.reads.forward
40 #set $reverse_reads = $single_paired.collection.reads.reverse 40 #set $reverse_reads = $single_paired.reads.reverse
41 #end if 41 #end if
42 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads) 42 #set $reads = "'%s' '%s'" % ($forward_reads, $reverse_reads)
43 $reads 43 $reads
44 #end if 44 #end if
45 $single_overhang 45 $single_overhang
57 <inputs> 57 <inputs>
58 <expand macro="reference_input" /> 58 <expand macro="reference_input" />
59 <conditional name="single_paired"> 59 <conditional name="single_paired">
60 <param name="single_paired_selector" type="select" label="Single-end or paired reads"> 60 <param name="single_paired_selector" type="select" label="Single-end or paired reads">
61 <option value="single" selected="true">Single-end</option> 61 <option value="single" selected="true">Single-end</option>
62 <option value="paired">Paired</option> 62 <option value="paired_single">Paired.end (individual files)</option>
63 <option value="paired_collection">Paired-end (collections)</option>
63 </param> 64 </param>
64 <when value="single"> 65 <when value="single">
65 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> 66 <param name="reads" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
66 <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" /> 67 <param argument="--fragment-length" type="integer" value="200" label="Average fragment length" help="Illumina typically produces reads of 180-200bp" />
67 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" /> 68 <param argument="--sd" type="integer" value="20" label="Estimated standard deviation of fragment length" />
68 </when> 69 </when>
69 <when value="paired"> 70 <when value="paired_single">
70 <conditional name="collection"> 71 <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" />
71 <param name="collection_selector" type="select" label="Collection or individual datasets"> 72 <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
72 <option value="datasets" selected="true">Individual files</option> 73 <expand macro="macro_lib_type"/>
73 <option value="collection">Pair or list of pairs</option> 74 </when>
74 </param> 75 <when value="paired_collection">
75 <when value="datasets"> 76 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
76 <param name="forward" type="data" format="fastq,fastq.gz" label="Forward reads" /> 77 <expand macro="macro_lib_type"/>
77 <param name="reverse" type="data" format="fastq,fastq.gz" label="Reverse reads" />
78 </when>
79 <when value="collection">
80 <param name="reads" type="data_collection" format="fastq,fastq.gz" collection_type="paired" label="Collection of reads" />
81 </when>
82 </conditional>
83 <param name="lib_type" type="select" label="Library strandness information">
84 <option value="">Unstranded</option>
85 <option value="--fr-stranded">Strand specific reads, first read forward</option>
86 <option value="--rf-stranded">Strand specific reads, first read reverse</option>
87 </param>
88 </when> 78 </when>
89 </conditional> 79 </conditional>
90 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" help="It allows to learn 80 <param argument="--bias" type="boolean" truevalue="--bias" falsevalue="" label="Perform sequence based bias correction" help="It allows to learn
91 parameters for a model of sequences specific bias and corrects the abundances accordlingly"/> 81 parameters for a model of sequences specific bias and corrects the abundances accordlingly"/>
92 <param argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="Running with bootstraps 82 <param argument="--bootstrap-samples" type="integer" value="0" label="Number of bootstrap samples" help="Running with bootstraps
121 </outputs> 111 </outputs>
122 <tests> 112 <tests>
123 <test> 113 <test>
124 <param name="reference_transcriptome_source" value="history" /> 114 <param name="reference_transcriptome_source" value="history" />
125 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 115 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
126 <param name="single_paired_selector" value="paired" /> 116 <param name="single_paired_selector" value="paired_single" />
127 <param name="collection_selector" value="datasets" />
128 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" /> 117 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
129 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> 118 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
130 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" /> 119 <output name="abundance_tab" file="kallisto_quant_out1.tab" ftype="tabular" />
131 </test> 120 </test>
132 <test> 121 <test>
133 <param name="reference_transcriptome_source" value="history" /> 122 <param name="reference_transcriptome_source" value="history" />
134 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 123 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
135 <param name="single_paired_selector" value="paired" /> 124 <param name="single_paired_selector" value="paired_single" />
136 <param name="collection_selector" value="datasets" />
137 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" /> 125 <param name="forward" ftype="fastq" value="mm10_chrM-1.f.fq" />
138 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" /> 126 <param name="reverse" ftype="fastq" value="mm10_chrM-1.r.fq" />
139 <param name="lib_type" value="--fr-stranded"/> 127 <param name="lib_type" value="--fr-stranded"/>
140 <output name="abundance_tab" > 128 <output name="abundance_tab" >
141 <assert_contents> 129 <assert_contents>
144 </output> 132 </output>
145 </test> 133 </test>
146 <test> 134 <test>
147 <param name="reference_transcriptome_source" value="history" /> 135 <param name="reference_transcriptome_source" value="history" />
148 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 136 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
149 <param name="single_paired_selector" value="paired" /> 137 <param name="single_paired_selector" value="paired_collection" />
150 <param name="collection_selector" value="collection" />
151 <param name="reads"> 138 <param name="reads">
152 <collection type="paired"> 139 <collection type="paired">
153 <element name="forward" value="mm10_chrM-1.f.fq" /> 140 <element name="forward" value="mm10_chrM-1.f.fq" />
154 <element name="reverse" value="mm10_chrM-1.r.fq" /> 141 <element name="reverse" value="mm10_chrM-1.r.fq" />
155 </collection> 142 </collection>
158 </test> 145 </test>
159 <test> 146 <test>
160 <param name="reference_transcriptome_source" value="history" /> 147 <param name="reference_transcriptome_source" value="history" />
161 <param name="reference" ftype="fasta" value="mm10_chrM.fa" /> 148 <param name="reference" ftype="fasta" value="mm10_chrM.fa" />
162 <param name="single_paired_selector" value="single" /> 149 <param name="single_paired_selector" value="single" />
163 <param name="collection_selector" value="collection" />
164 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" /> 150 <param name="reads" ftype="fastq" value="mm10_chrM-1.f.fq" />
165 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" /> 151 <output name="abundance_tab" file="kallisto_quant_out3.tab" ftype="tabular" />
166 </test> 152 </test>
167 <test> 153 <test>
168 <param name="reference_transcriptome_source" value="history" /> 154 <param name="reference_transcriptome_source" value="history" />
169 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" /> 155 <param name="reference" ftype="fasta" value="felCat8_chrM.fa" />
170 <param name="single_paired_selector" value="paired" /> 156 <param name="single_paired_selector" value="paired_single" />
171 <param name="collection_selector" value="datasets" />
172 <param name="pseudobam" value="true" /> 157 <param name="pseudobam" value="true" />
173 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" /> 158 <param name="forward" ftype="fastq" value="felCat8_chrM_F.fq" />
174 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" /> 159 <param name="reverse" ftype="fastq" value="felCat8_chrM_R.fq" />
175 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" /> 160 <output name="abundance_tab" file="kallisto_quant_out4.tab" ftype="tabular" />
176 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/> 161 <output name="pseudobam_output" file="kallisto_quant_out4.bam" ftype="bam" lines_diff="2"/>
177 </test> 162 </test>
178 <test> 163 <test>
179 <param name="reference_transcriptome_source" value="cached" /> 164 <param name="reference_transcriptome_source" value="cached" />
180 <param name="single_paired_selector" value="paired" /> 165 <param name="single_paired_selector" value="paired_single" />
181 <param name="collection_selector" value="datasets" />
182 <param name="pseudobam" value="true" /> 166 <param name="pseudobam" value="true" />
183 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" /> 167 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
184 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" /> 168 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq" />
185 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" /> 169 <output name="abundance_tab" file="kallisto_quant_out5.tab" ftype="tabular" />
186 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/> 170 <output name="pseudobam_output" file="kallisto_quant_out5.bam" ftype="bam" lines_diff="2"/>
187 </test> 171 </test>
188 <test> 172 <test>
189 <param name="reference_transcriptome_source" value="history" /> 173 <param name="reference_transcriptome_source" value="history" />
190 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" /> 174 <param name="reference" ftype="fasta" value="hg38_transcripts.fa" />
191 <param name="single_paired_selector" value="paired" /> 175 <param name="single_paired_selector" value="paired_single" />
192 <param name="collection_selector" value="datasets" />
193 <param name="fusion" value="true" /> 176 <param name="fusion" value="true" />
194 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" /> 177 <param name="forward" ftype="fastq" dbkey="hg38" value="hg38_F.fq.gz" />
195 <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" /> 178 <param name="reverse" ftype="fastq" dbkey="hg38" value="hg38_R.fq.gz" />
196 <output name="fusion_output" file="fusion.txt" ftype="tabular" /> 179 <output name="fusion_output" file="fusion.txt" ftype="tabular" />
197 </test> 180 </test>
198 <test> 181 <test>
199 <param name="reference_transcriptome_source" value="history" /> 182 <param name="reference_transcriptome_source" value="history" />
200 <param name="reference" ftype="fasta" value="transcripts.fasta" /> 183 <param name="reference" ftype="fasta" value="transcripts.fasta" />
201 <param name="single_paired_selector" value="paired" /> 184 <param name="single_paired_selector" value="paired_single" />
202 <param name="collection_selector" value="datasets" />
203 <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" /> 185 <param name="forward" ftype="fastq" value="reads_forward.fastq.gz" />
204 <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" /> 186 <param name="reverse" ftype="fastq" value="reads_reverse.fastq.gz" />
205 <conditional name="genomebam_option"> 187 <conditional name="genomebam_option">
206 <param name="selector" value="--genomebam"/> 188 <param name="selector" value="--genomebam"/>
207 <param name="gtf" value="annotation.gtf.gz"/> 189 <param name="gtf" value="annotation.gtf.gz"/>