Mercurial > repos > iuc > stacks_denovomap
comparison stacks_denovomap.xml @ 5:34000c653ae5 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 9401451df4a985ef5686864eaadafa077ffc0877
| author | iuc |
|---|---|
| date | Mon, 27 Feb 2017 05:43:39 -0500 |
| parents | 998dfec32bde |
| children | 39d2b6c1c030 |
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| 4:998dfec32bde | 5:34000c653ae5 |
|---|---|
| 10 #import re | 10 #import re |
| 11 | 11 |
| 12 #if str( $options_usage.rad_analysis_type ) == "genetic": | 12 #if str( $options_usage.rad_analysis_type ) == "genetic": |
| 13 #for $input_parent in $options_usage.parent_sequences: | 13 #for $input_parent in $options_usage.parent_sequences: |
| 14 | 14 |
| 15 #if $input_parent.ext == "fastqsanger": | 15 #if $input_parent.is_of_type('fastqsanger'): |
| 16 #set $data_path = splitext($input_parent.element_identifier)[0] | 16 #set $data_path = splitext($input_parent.element_identifier)[0] |
| 17 #set $data_path = re.sub(r'\.1$', '', $data_path) | 17 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 18 #set $data_path = $data_path + ".fq" | 18 #set $data_path = $data_path + ".fq" |
| 19 #else: | 19 #else: |
| 20 #set $data_path = splitext($input_parent.element_identifier)[0] | 20 #set $data_path = splitext($input_parent.element_identifier)[0] |
| 25 ln -s "${input_parent}" "${data_path}" && | 25 ln -s "${input_parent}" "${data_path}" && |
| 26 #end for | 26 #end for |
| 27 | 27 |
| 28 #for $input_progeny in $options_usage.progeny_sequences: | 28 #for $input_progeny in $options_usage.progeny_sequences: |
| 29 #if $input_progeny: | 29 #if $input_progeny: |
| 30 #if $input_progeny.ext == "fastqsanger": | 30 #if $input_progeny.is_of_type('fastqsanger'): |
| 31 #set $data_path = splitext($input_progeny.element_identifier)[0] | 31 #set $data_path = splitext($input_progeny.element_identifier)[0] |
| 32 #set $data_path = re.sub(r'\.1$', '', $data_path) | 32 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 33 #set $data_path = $data_path + ".fq" | 33 #set $data_path = $data_path + ".fq" |
| 34 #else: | 34 #else: |
| 35 #set $data_path = splitext($input_progeny.element_identifier)[0] | 35 #set $data_path = splitext($input_progeny.element_identifier)[0] |
| 41 #end if | 41 #end if |
| 42 #end for | 42 #end for |
| 43 #else: | 43 #else: |
| 44 #for $input_indiv in $options_usage.individual_sample: | 44 #for $input_indiv in $options_usage.individual_sample: |
| 45 | 45 |
| 46 #if $input_indiv.ext == "fastqsanger": | 46 #if $input_indiv.is_of_type('fastqsanger'): |
| 47 #set $data_path = splitext($input_indiv.element_identifier)[0] | 47 #set $data_path = splitext($input_indiv.element_identifier)[0] |
| 48 #set $data_path = re.sub(r'\.1$', '', $data_path) | 48 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 49 #set $data_path = $data_path + ".fq" | 49 #set $data_path = $data_path + ".fq" |
| 50 #else: | 50 #else: |
| 51 #set $data_path = splitext($input_indiv.element_identifier)[0] | 51 #set $data_path = splitext($input_indiv.element_identifier)[0] |
| 65 | 65 |
| 66 -T \${GALAXY_SLOTS:-1} | 66 -T \${GALAXY_SLOTS:-1} |
| 67 | 67 |
| 68 #if str( $options_usage.rad_analysis_type ) == "genetic": | 68 #if str( $options_usage.rad_analysis_type ) == "genetic": |
| 69 #for $input_parent in $options_usage.parent_sequences: | 69 #for $input_parent in $options_usage.parent_sequences: |
| 70 #if $input_parent.ext == "fastqsanger": | 70 #if $input_parent.is_of_type('fastqsanger'): |
| 71 #set $data_path = splitext($input_parent.element_identifier)[0] | 71 #set $data_path = splitext($input_parent.element_identifier)[0] |
| 72 #set $data_path = re.sub(r'\.1$', '', $data_path) | 72 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 73 #set $data_path = $data_path + ".fq" | 73 #set $data_path = $data_path + ".fq" |
| 74 #else: | 74 #else: |
| 75 #set $data_path = splitext($input_parent.element_identifier)[0] | 75 #set $data_path = splitext($input_parent.element_identifier)[0] |
| 82 | 82 |
| 83 -A $options_usage.cross_type | 83 -A $options_usage.cross_type |
| 84 | 84 |
| 85 #for $input_progeny in $options_usage.progeny_sequences: | 85 #for $input_progeny in $options_usage.progeny_sequences: |
| 86 #if $input_progeny: | 86 #if $input_progeny: |
| 87 #if $input_progeny.ext == "fastqsanger": | 87 #if $input_progeny.is_of_type('fastqsanger'): |
| 88 #set $data_path = splitext($input_progeny.element_identifier)[0] | 88 #set $data_path = splitext($input_progeny.element_identifier)[0] |
| 89 #set $data_path = re.sub(r'\.1$', '', $data_path) | 89 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 90 #set $data_path = $data_path + ".fq" | 90 #set $data_path = $data_path + ".fq" |
| 91 #else: | 91 #else: |
| 92 #set $data_path = splitext($input_progeny.element_identifier)[0] | 92 #set $data_path = splitext($input_progeny.element_identifier)[0] |
| 102 -P $assembly_options.P | 102 -P $assembly_options.P |
| 103 #end if | 103 #end if |
| 104 #else: | 104 #else: |
| 105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample): | 105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample): |
| 106 | 106 |
| 107 #if $input_indiv.ext == "fastqsanger": | 107 #if $input_indiv.is_of_type('fastqsanger'): |
| 108 #set $data_path = splitext($input_indiv.element_identifier)[0] | 108 #set $data_path = splitext($input_indiv.element_identifier)[0] |
| 109 #set $data_path = re.sub(r'\.1$', '', $data_path) | 109 #set $data_path = re.sub(r'\.1$', '', $data_path) |
| 110 #set $data_path = $data_path + ".fq" | 110 #set $data_path = $data_path + ".fq" |
| 111 #else: | 111 #else: |
| 112 #set $data_path = splitext($input_indiv.element_identifier)[0] | 112 #set $data_path = splitext($input_indiv.element_identifier)[0] |