Mercurial > repos > lparsons > htseq_count

comparison htseq-count.xml @ 27:67b0b160903a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
author iuc
date Thu, 17 Oct 2019 03:01:55 -0400
parents 7f5a8d427b39
children 916cb26bd9d3
comparison
equal deleted inserted replaced
26:7f5a8d427b39 27:67b0b160903a
30 #end if 30 #end if
31 #end if 31 #end if
32 #end if 32 #end if
33 33
34 #if $samfile.extension == 'bam': 34 #if $samfile.extension == 'bam':
35 samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' && 35 samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' '$samfile' &&
36 #else 36 #else
37 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n --output-fmt=SAM -o '$name_sorted_alignment_filename' - && 37 samtools view -Su -t '${reference_fasta_filename}.fai' '$samfile' | samtools sort -n -T "\${TMPDIR:-.}" --output-fmt=SAM -o '$name_sorted_alignment_filename' - &&
38 #end if 38 #end if
39 39
40 htseq-count 40 htseq-count
41 --mode=$mode 41 --mode=$mode
42 --stranded=$stranded 42 --stranded=$stranded
64 #if str( $advanced_options.advanced_options_selector ) == "advanced": 64 #if str( $advanced_options.advanced_options_selector ) == "advanced":
65 #if $advanced_options.samout_conditional.samout == "Yes": 65 #if $advanced_options.samout_conditional.samout == "Yes":
66 && samtools view -Su 66 && samtools view -Su
67 -t '${reference_fasta_filename}.fai' 67 -t '${reference_fasta_filename}.fai'
68 '$__new_file_path__/${samoutfile.id}_tmp.sam' 68 '$__new_file_path__/${samoutfile.id}_tmp.sam'
69 | samtools sort -o '$samoutfile' - 69 | samtools sort -T "\${TMPDIR:-.}" -o '$samoutfile' -
70 #end if 70 #end if
71 #end if 71 #end if
72 ]]> 72 ]]>
73 </command> 73 </command>
74 74
126 <option value="history">History</option> 126 <option value="history">History</option>
127 </param> 127 </param>
128 <when value="cached"> 128 <when value="cached">
129 <param name="ref_file" type="select" label="Using reference genome"> 129 <param name="ref_file" type="select" label="Using reference genome">
130 <options from_data_table="sam_fa_indexes"> 130 <options from_data_table="sam_fa_indexes">
131 <filter type="data_meta" key="dbkey" ref="samfile" column="1"/> 131 <filter type="data_meta" key="dbkey" ref="samfile" column="value"/>
132 </options> 132 </options>
133 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 133 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
134 </param> 134 </param>
135 </when> 135 </when>
136 <when value="history"> 136 <when value="history">