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comparison samtools_view.xml @ 14:e63aab0f18c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 5cb103832529f17e5c72e7f122758c13519fbe5e
author iuc
date Mon, 15 Aug 2022 09:13:14 +0000
parents ef12d752aba9
children e41d3ce2ab9f
comparison
equal deleted inserted replaced
13:ef12d752aba9 14:e63aab0f18c6
1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@"> 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> 2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@REF_DATA@"> 5 <token name="@REF_DATA@">
6 ## additional reference data 6 ## additional reference data
152 #if $input.is_of_type('sam') or $std_filters or $reg_filters: 152 #if $input.is_of_type('sam') or $std_filters or $reg_filters:
153 ## There is no index or we cannot use it because we are 153 ## There is no index or we cannot use it because we are
154 ## not dealing with all of the reads in the indexed 154 ## not dealing with all of the reads in the indexed
155 ## file. We have to do an extra pass over the input to 155 ## file. We have to do an extra pass over the input to
156 ## count the reads to subsample. 156 ## count the reads to subsample.
157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && 157 sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
158 #else: 158 #else:
159 ## We can get the count of reads to subsample using 159 ## We can get the count of reads to subsample using
160 ## an inexpensive call to idxstats. 160 ## an inexpensive call to idxstats.
161 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; print(frac > 1 ? $seed+1/frac : ".0")}'` && 161 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
162 #end if 162 #end if
163 #end if 163 #end if
164 #end if 164 #end if
165 165
166 ## call samtools view 166 ## call samtools view
688 <param name="addref_select" value="history" /> 688 <param name="addref_select" value="history" />
689 <param name="ref" value="test.fa" /> 689 <param name="ref" value="test.fa" />
690 </conditional> 690 </conditional>
691 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" /> 691 <output name="outputsam" file="test_20.bam" ftype="bam" lines_diff="4" />
692 </test> 692 </test>
693 <!-- 21) sampling options--> 693 <!-- 21) sampling options target < total reads -->
694 <test> 694 <test>
695 <param name="input" value="in_test_15.sam" ftype="sam" /> 695 <param name="input" value="in_test_15.sam" ftype="sam" />
696 <conditional name="mode"> 696 <conditional name="mode">
697 <param name="outtype" value="selected_reads" /> 697 <param name="outtype" value="selected_reads" />
698 <section name="subsample_config"> 698 <section name="subsample_config">
705 <conditional name="output_format"> 705 <conditional name="output_format">
706 <param name="oformat" value="input" /> 706 <param name="oformat" value="input" />
707 </conditional> 707 </conditional>
708 </conditional> 708 </conditional>
709 </conditional> 709 </conditional>
710 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="6" /> 710 <output name="outputsam" file="test_21.sam" ftype="sam" compare="diff" lines_diff="10" />
711 </test> 711 </test>
712 <!-- 22) --> 712 <!-- 22) target > total reads -->
713 <test> 713 <test>
714 <param name="input" value="in_test_15.sam" ftype="sam" /> 714 <param name="input" value="in_test_15.sam" ftype="sam" />
715 <conditional name="mode"> 715 <conditional name="mode">
716 <param name="outtype" value="selected_reads" /> 716 <param name="outtype" value="selected_reads" />
717 <section name="subsample_config"> 717 <section name="subsample_config">
784 <conditional name="output_format"> 784 <conditional name="output_format">
785 <param name="oformat" value="input" /> 785 <param name="oformat" value="input" />
786 </conditional> 786 </conditional>
787 </conditional> 787 </conditional>
788 </conditional> 788 </conditional>
789 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="6" /> 789 <output name="outputsam" file="test_25.sam" ftype="sam" compare="diff" lines_diff="2" />
790 </test> 790 </test>
791 <!-- 26) --> 791 <!-- 26) -->
792 <test> 792 <test>
793 <param name="input" value="in_test_14.bam" ftype="bam" /> 793 <param name="input" value="in_test_14.bam" ftype="bam" />
794 <conditional name="mode"> 794 <conditional name="mode">