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comparison dexseq_count.xml @ 18:ffa256d657b2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
author iuc
date Fri, 31 Jan 2025 18:00:29 +0000
parents d104044e4257
children
comparison
equal deleted inserted replaced
17:d104044e4257 18:ffa256d657b2
14 <regex match="Exception:" /> 14 <regex match="Exception:" />
15 </stdio> 15 </stdio>
16 <command><![CDATA[ 16 <command><![CDATA[
17 #if $mode.mode_select == "prepare": 17 #if $mode.mode_select == "prepare":
18 dexseq_prepare_annotation.py 18 dexseq_prepare_annotation.py
19 -r $mode.aggregate 19 -r '${mode.aggregate}'
20 '$mode.gtffile' 20 '${mode.gtffile}'
21 '$flattened_gtf_out' 21 '$flattened_gtf_out'
22 #elif $mode.mode_select == "count": 22 #elif $mode.mode_select == "count":
23 ln -s -f '${mode.bamfile}' 'input.bam' &&
24 ln -s -f '${mode.bamfile.metadata.bam_index}' 'input.bam.bai' &&
23 dexseq_count.py 25 dexseq_count.py
24 --format bam 26 --format bam
25 --paired $mode.paired 27 --paired '${mode.paired}'
26 --stranded $mode.stranded 28 --stranded '${mode.stranded}'
27 --minaqual $mode.qual 29 --minaqual '${mode.qual}'
28 --order $mode.order 30 --order '${mode.order}'
29 $mode.flattened_gtf_in 31 '${mode.flattened_gtf_in}'
30 '$mode.bamfile' 32 'input.bam'
31 '$counts_file' 33 '$counts_file'
32 && 34 &&
33 sed -i 's/\"//g' '$counts_file' 35 sed -i 's/\"//g' '$counts_file'
34 #end if 36 #end if
35 ]]></command> 37 ]]></command>
71 <filter>mode['mode_select'] == 'prepare'</filter> 73 <filter>mode['mode_select'] == 'prepare'</filter>
72 </data> 74 </data>
73 </outputs> 75 </outputs>
74 76
75 <tests> 77 <tests>
76 <test> 78 <test expect_num_outputs="1">
77 <param name="mode_select" value="prepare" /> 79 <param name="mode_select" value="prepare" />
78 <param name="gtffile" ftype="gff" value="original.gtf"/> 80 <param name="gtffile" ftype="gff" value="original.gtf"/>
79 <param name="aggregate" value="True"/> 81 <param name="aggregate" value="True"/>
80 <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/> 82 <output name="flattened_gtf_out" ftype="gtf" compare="sim_size" file="flattened.gtf"/>
81 </test> 83 </test>
82 <!-- Ensure count mode works --> 84 <!-- Ensure count mode works -->
83 <test> 85 <test expect_num_outputs="1">
84 <param name="mode_select" value="count" /> 86 <param name="mode_select" value="count" />
85 <param name="bamfile" ftype="bam" value="in.bam" /> 87 <param name="bamfile" ftype="bam" value="in.bam" />
86 <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/> 88 <param name="flattened_gtf_in" ftype="gff" value="flattened.gtf"/>
87 <param name="stranded" value="no" /> 89 <param name="stranded" value="no" />
88 <output name="counts_file" ftype="tabular" file="out_count.tab"/> 90 <output name="counts_file" ftype="tabular" file="out_count.tab"/>