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comparison kallisto_pseudo.xml @ 3:5ae5c312d718 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f84c314bc721b5b0c7be10eaf287b1830caca241"
author iuc
date Thu, 26 Sep 2019 09:11:24 -0400
parents 1c75aa5de15e
children 01247aaf0a10
comparison
equal deleted inserted replaced
2:1c75aa5de15e 3:5ae5c312d718
13 #set index_path = 'reference.kallisto' 13 #set index_path = 'reference.kallisto'
14 #else: 14 #else:
15 #set index_path = $reference_transcriptome.index.fields.path 15 #set index_path = $reference_transcriptome.index.fields.path
16 #end if 16 #end if
17 kallisto pseudo -i '$index_path' 17 kallisto pseudo -i '$index_path'
18 #if $pseudobam: 18 --threads \${GALAXY_SLOTS:-1}
19 $pseudobam -o . 19 -o .
20 #else:
21 --threads \${GALAXY_SLOTS:-1}
22 -o .
23 #end if
24
25 20
26 #if str($single_paired.single_paired_selector) == 'single': 21 #if str($single_paired.single_paired_selector) == 'single':
27 --single --fragment-length $single_paired.fragment_length 22 --single --fragment-length $single_paired.fragment_length
28 --sd $single_paired.sd '$single_paired.reads' 23 --sd $single_paired.sd '$single_paired.reads'
29 #else: 24 #else:
37 '$single_paired.collection.fastq_umi.forward' 32 '$single_paired.collection.fastq_umi.forward'
38 '$single_paired.collection.fastq_umi.reverse' 33 '$single_paired.collection.fastq_umi.reverse'
39 #end if 34 #end if
40 #end if 35 #end if
41 #end if 36 #end if
42 #if $pseudobam:
43 | samtools sort -O bam -@ \${GALAXY_SLOTS:-1} -o '$pseudobam_output' -
44 #end if
45 && if [ -f run_info.json ] ; then cat run_info.json ; fi && 37 && if [ -f run_info.json ] ; then cat run_info.json ; fi &&
46 mkdir outputs && 38 mkdir outputs &&
47 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi && 39 if [ -f matrix.ec ] ; then mv matrix.ec outputs/Matrix.ec ; fi &&
48 if [ -f matrix.tsv ] ; then mv matrix.tsv outputs/Matrix.tabular ; fi && 40 if [ -f matrix.tcc.mtx ] ; then mv matrix.tcc.mtx outputs/Matrix.tabular ; fi &&
49 if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi && 41 if [ -f matrix.cells ] ; then mv matrix.cells outputs/Matrix.cells ; fi &&
50 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi && 42 if [ -f pseudoalignments.tsv ] ; then mv pseudoalignments.tsv outputs/Pseudoalignments.tabular ; fi &&
51 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi 43 if [ -f pseudoalignments.ec ] ; then mv pseudoalignments.ec outputs/Pseudoalignments.ec ; fi
52 ]]> 44 ]]>
53 </command> 45 </command>
104 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" /> 96 <param name="reads" type="data_collection" format="fastq" collection_type="paired" label="Collection of reads" />
105 </when> 97 </when>
106 </conditional> 98 </conditional>
107 </when> 99 </when>
108 </conditional> 100 </conditional>
109 <param argument="--pseudobam" type="boolean" truevalue="--pseudobam" falsevalue="" label="Output pseudoalignments in BAM format" />
110 </inputs> 101 </inputs>
111 <outputs> 102 <outputs>
112 <data format="tabular" name="sample"> 103 <data format="tabular" name="sample">
113 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" /> 104 <discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="outputs" ext="tabular" visible="true" />
114 </data>
115 <data format="bam" name="pseudobam_output" label="${tool.name} on ${on_string}: Pseudoalignments (BAM)">
116 <filter>pseudobam</filter>
117 </data> 105 </data>
118 </outputs> 106 </outputs>
119 <tests> 107 <tests>
120 <test> 108 <test>
121 <param name="reference_transcriptome_source" value="history" /> 109 <param name="reference_transcriptome_source" value="history" />
174 </test> 162 </test>
175 <test> 163 <test>
176 <param name="reference_transcriptome_source" value="cached" /> 164 <param name="reference_transcriptome_source" value="cached" />
177 <param name="single_paired_selector" value="paired" /> 165 <param name="single_paired_selector" value="paired" />
178 <param name="collection_selector" value="datasets" /> 166 <param name="collection_selector" value="datasets" />
179 <param name="pseudobam" value="true" />
180 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_F.fq.gz" />
181 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
182 <output name="sample">
183 <discovered_dataset designation="Pseudoalignments.tabular" file="kallisto_pseudo_out5.tab" ftype="tabular" />
184 <discovered_dataset designation="Pseudoalignments.ec" file="kallisto_pseudo_out5.ec" ftype="tabular" />
185 </output>
186 <output name="pseudobam_output" file="kallisto_pseudo_out5.bam" ftype="bam" />
187 </test>
188 <test>
189 <param name="reference_transcriptome_source" value="cached" />
190 <param name="single_paired_selector" value="paired" />
191 <param name="collection_selector" value="datasets" />
192 <param name="umi" value="yes" /> 167 <param name="umi" value="yes" />
193 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" /> 168 <param name="forward" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM.umi" />
194 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" /> 169 <param name="reverse" ftype="fastq" dbkey="sacCer2" value="sacCer2_chrM_R.fq.gz" />
195 <output name="sample"> 170 <output name="sample">
196 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" /> 171 <discovered_dataset designation="Matrix.tabular" file="kallisto_pseudo_out6.tab" ftype="tabular" />