Mercurial > repos > iuc > isoformswitchanalyzer

comparison isoformswitchanalyzer.xml @ 1:5ae218cee629 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7d278967f9c8d2c6ce0a8f83be2c444822746bbf
author iuc
date Fri, 19 May 2023 21:25:39 +0000
parents bb611fa3bc3b
children db30020fee5b
comparison
equal deleted inserted replaced
0:bb611fa3bc3b 1:5ae218cee629
23 #if $functionMode.selector == 'data_import' 23 #if $functionMode.selector == 'data_import'
24 #if $functionMode.transcriptome.is_of_type("fasta.gz"): 24 #if $functionMode.transcriptome.is_of_type("fasta.gz"):
25 ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' && 25 ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' &&
26 #set $transcriptome = './transcriptome.fasta.gz' 26 #set $transcriptome = './transcriptome.fasta.gz'
27 #else 27 #else
28 ln -s '${functionMode.transcriptome}' './transcriptome.fasta' 28 ln -s '${functionMode.transcriptome}' './transcriptome.fasta' &&
29 #set $transcriptome = './transcriptome.fasta' 29 #set $transcriptome = './transcriptome.fasta'
30 #end if 30 #end if
31 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"): 31 #if $functionMode.genomeAnnotation.is_of_type("gtf.gz"):
32 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf.gz' && 32 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf.gz' &&
33 #set $annotation = './annotation.gtf.gz' 33 #set $annotation = './annotation.gtf.gz'
34 #else 34 #else
35 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' && 35 ln -s '${functionMode.genomeAnnotation}' './annotation.gtf' &&
36 #set $annotation = './annotation.gtf' 36 #set $annotation = './annotation.gtf'
37 #end if 37 #end if
38 mkdir -p 'input_files' && 38 mkdir -p 'input_files' &&
39 #if $functionMode.countFiles != 'disabled': 39 #if $functionMode.countFiles != 'disabled':
40 mkdir -p "count_files/factor1/" && 40 mkdir -p "count_files/factor1/" &&
41 mkdir -p "count_files/factor2/" && 41 mkdir -p "count_files/factor2/" &&
764 <has_size value="6361" delta="300"/> 764 <has_size value="6361" delta="300"/>
765 </assert_contents> 765 </assert_contents>
766 </element> 766 </element>
767 <element name="splicingGenomewide" ftype="pdf"> 767 <element name="splicingGenomewide" ftype="pdf">
768 <assert_contents> 768 <assert_contents>
769 <has_size value="68069" delta="300"/> 769 <has_size value="165752" delta="300"/>
770 </assert_contents> 770 </assert_contents>
771 </element> 771 </element>
772 <element name="splicingSummary" ftype="pdf"> 772 <element name="splicingSummary" ftype="pdf">
773 <assert_contents> 773 <assert_contents>
774 <has_size value="5990" delta="300"/> 774 <has_size value="5990" delta="300"/>
775 </assert_contents> 775 </assert_contents>
776 </element> 776 </element>
777 <element name="switchGene" ftype="pdf"> 777 <element name="switchGene" ftype="pdf">
778 <assert_contents> 778 <assert_contents>
779 <has_size value="3611" delta="300"/> 779 <has_size value="18432" delta="300"/>
780 </assert_contents> 780 </assert_contents>
781 </element> 781 </element>
782 <element name="volcanoPlot" ftype="pdf"> 782 <element name="volcanoPlot" ftype="pdf">
783 <assert_contents> 783 <assert_contents>
784 <has_size value="3611" delta="300"/> 784 <has_size value="20147" delta="300"/>
785 </assert_contents> 785 </assert_contents>
786 </element> 786 </element>
787 </output_collection> 787 </output_collection>
788 <output_collection name="genes_consequences" type="list" count="2"> 788 <output_collection name="genes_consequences" type="list" count="2">
789 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf"> 789 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">
893 <has_size value="6361" delta="300"/> 893 <has_size value="6361" delta="300"/>
894 </assert_contents> 894 </assert_contents>
895 </element> 895 </element>
896 <element name="splicingGenomewide" ftype="pdf"> 896 <element name="splicingGenomewide" ftype="pdf">
897 <assert_contents> 897 <assert_contents>
898 <has_size value="68069" delta="300"/> 898 <has_size value="165752" delta="300"/>
899 </assert_contents> 899 </assert_contents>
900 </element> 900 </element>
901 <element name="splicingSummary" ftype="pdf"> 901 <element name="splicingSummary" ftype="pdf">
902 <assert_contents> 902 <assert_contents>
903 <has_size value="5990" delta="300"/> 903 <has_size value="5990" delta="300"/>
904 </assert_contents> 904 </assert_contents>
905 </element> 905 </element>
906 <element name="switchGene" ftype="pdf"> 906 <element name="switchGene" ftype="pdf">
907 <assert_contents> 907 <assert_contents>
908 <has_size value="3611" delta="300"/> 908 <has_size value="18432" delta="300"/>
909 </assert_contents> 909 </assert_contents>
910 </element> 910 </element>
911 <element name="volcanoPlot" ftype="pdf"> 911 <element name="volcanoPlot" ftype="pdf">
912 <assert_contents> 912 <assert_contents>
913 <has_size value="3611" delta="300"/> 913 <has_size value="20147" delta="300"/>
914 </assert_contents> 914 </assert_contents>
915 </element> 915 </element>
916 </output_collection> 916 </output_collection>
917 <output_collection name="genes_consequences" type="list" count="2"> 917 <output_collection name="genes_consequences" type="list" count="2">
918 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf"> 918 <element name="1_switch_plot_NADK_aka_NADK" ftype="pdf">