Mercurial > repos > drosofff > msp_sr_readmap_and_size_histograms
changeset 7:9784e5046f04 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 450d1b3d954cc7d96e53652d468811546951f995
| author | drosofff |
|---|---|
| date | Thu, 26 Nov 2015 11:55:39 -0500 |
| parents | 0f7cf7fb3465 |
| children | 4e7f59d5ee18 |
| files | readmap.xml smRtools.pyc tool_dependencies.xml |
| diffstat | 3 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/readmap.xml Wed Oct 21 11:12:45 2015 -0400 +++ b/readmap.xml Thu Nov 26 11:55:39 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.4"> +<tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.0.5"> <description>from sRbowtie aligment</description> <requirements> <requirement type="package" version="0.12.7">bowtie</requirement> @@ -157,8 +157,10 @@ ## GRAPHS if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else { - rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } - if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test + rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 } + ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 } + ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 } + if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width) for (i in seq(1,n_genes,rows_per_page)) {
--- a/tool_dependencies.xml Wed Oct 21 11:12:45 2015 -0400 +++ b/tool_dependencies.xml Thu Nov 26 11:55:39 2015 -0500 @@ -7,7 +7,7 @@ <repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="numpy" version="1.9"> - <repository changeset_revision="816d3480b0b1" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f9289486f06d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.1.2"> <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />